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ajenhl/tacl
tacl/sequence.py
Sequence._format_alignment
def _format_alignment(self, a1, a2): """Returns `a1` marked up with HTML spans around characters that are also at the same index in `a2`. :param a1: text sequence from one witness :type a1: `str` :param a2: text sequence from another witness :type a2: `str` :rtype: `str` """ html = [] for index, char in enumerate(a1): output = self._substitutes.get(char, char) if a2[index] == char: html.append('<span class="match">{}</span>'.format(output)) elif char != '-': html.append(output) return ''.join(html)
python
def _format_alignment(self, a1, a2): """Returns `a1` marked up with HTML spans around characters that are also at the same index in `a2`. :param a1: text sequence from one witness :type a1: `str` :param a2: text sequence from another witness :type a2: `str` :rtype: `str` """ html = [] for index, char in enumerate(a1): output = self._substitutes.get(char, char) if a2[index] == char: html.append('<span class="match">{}</span>'.format(output)) elif char != '-': html.append(output) return ''.join(html)
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Returns `a1` marked up with HTML spans around characters that are also at the same index in `a2`. :param a1: text sequence from one witness :type a1: `str` :param a2: text sequence from another witness :type a2: `str` :rtype: `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/sequence.py#L24-L42
train
48,400
ajenhl/tacl
tacl/sequence.py
Sequence.render
def render(self): """Returns a tuple of HTML fragments rendering each element of the sequence.""" f1 = self._format_alignment(self._alignment[0], self._alignment[1]) f2 = self._format_alignment(self._alignment[1], self._alignment[0]) return f1, f2
python
def render(self): """Returns a tuple of HTML fragments rendering each element of the sequence.""" f1 = self._format_alignment(self._alignment[0], self._alignment[1]) f2 = self._format_alignment(self._alignment[1], self._alignment[0]) return f1, f2
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Returns a tuple of HTML fragments rendering each element of the sequence.
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/sequence.py#L44-L49
train
48,401
ajenhl/tacl
tacl/sequence.py
SequenceReport.generate
def generate(self, output_dir, minimum_size): """Generates sequence reports and writes them to the output directory. :param output_dir: directory to output reports to :type output_dir: `str` :param minimum_size: minimum size of n-grams to create sequences for :type minimum_size: `int` """ self._output_dir = output_dir # Get a list of the files in the matches, grouped by label # (ordered by number of works). labels = list(self._matches.groupby([constants.LABEL_FIELDNAME])[ constants.WORK_FIELDNAME].nunique().index) original_ngrams = self._matches[ self._matches[ constants.SIZE_FIELDNAME] >= minimum_size].sort_values( by=constants.SIZE_FIELDNAME, ascending=False)[ constants.NGRAM_FIELDNAME].unique() ngrams = [] for original_ngram in original_ngrams: ngrams.append(self._get_text(Text(original_ngram, self._tokenizer))) # Generate sequences for each witness in every combination of # (different) labels. for index, primary_label in enumerate(labels): for secondary_label in labels[index+1:]: self._generate_sequences(primary_label, secondary_label, ngrams)
python
def generate(self, output_dir, minimum_size): """Generates sequence reports and writes them to the output directory. :param output_dir: directory to output reports to :type output_dir: `str` :param minimum_size: minimum size of n-grams to create sequences for :type minimum_size: `int` """ self._output_dir = output_dir # Get a list of the files in the matches, grouped by label # (ordered by number of works). labels = list(self._matches.groupby([constants.LABEL_FIELDNAME])[ constants.WORK_FIELDNAME].nunique().index) original_ngrams = self._matches[ self._matches[ constants.SIZE_FIELDNAME] >= minimum_size].sort_values( by=constants.SIZE_FIELDNAME, ascending=False)[ constants.NGRAM_FIELDNAME].unique() ngrams = [] for original_ngram in original_ngrams: ngrams.append(self._get_text(Text(original_ngram, self._tokenizer))) # Generate sequences for each witness in every combination of # (different) labels. for index, primary_label in enumerate(labels): for secondary_label in labels[index+1:]: self._generate_sequences(primary_label, secondary_label, ngrams)
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Generates sequence reports and writes them to the output directory. :param output_dir: directory to output reports to :type output_dir: `str` :param minimum_size: minimum size of n-grams to create sequences for :type minimum_size: `int`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/sequence.py#L68-L96
train
48,402
ajenhl/tacl
tacl/sequence.py
SequenceReport._generate_sequences
def _generate_sequences(self, primary_label, secondary_label, ngrams): """Generates aligned sequences between each witness labelled `primary_label` and each witness labelled `secondary_label`, based around `ngrams`. :param primary_label: label for one side of the pairs of witnesses to align :type primary_label: `str` :param secondary_label: label for the other side of the pairs of witnesses to align :type secondary_label: `str` :param ngrams: n-grams to base sequences off :type ngrams: `list` of `str` """ cols = [constants.WORK_FIELDNAME, constants.SIGLUM_FIELDNAME] primary_works = self._matches[self._matches[ constants.LABEL_FIELDNAME] == primary_label][ cols].drop_duplicates() secondary_works = self._matches[self._matches[ constants.LABEL_FIELDNAME] == secondary_label][ cols].drop_duplicates() for index, (work1, siglum1) in primary_works.iterrows(): text1 = self._get_text(self._corpus.get_witness(work1, siglum1)) label1 = '{}_{}'.format(work1, siglum1) for index, (work2, siglum2) in secondary_works.iterrows(): text2 = self._get_text(self._corpus.get_witness( work2, siglum2)) label2 = '{}_{}'.format(work2, siglum2) self._generate_sequences_for_texts(label1, text1, label2, text2, ngrams)
python
def _generate_sequences(self, primary_label, secondary_label, ngrams): """Generates aligned sequences between each witness labelled `primary_label` and each witness labelled `secondary_label`, based around `ngrams`. :param primary_label: label for one side of the pairs of witnesses to align :type primary_label: `str` :param secondary_label: label for the other side of the pairs of witnesses to align :type secondary_label: `str` :param ngrams: n-grams to base sequences off :type ngrams: `list` of `str` """ cols = [constants.WORK_FIELDNAME, constants.SIGLUM_FIELDNAME] primary_works = self._matches[self._matches[ constants.LABEL_FIELDNAME] == primary_label][ cols].drop_duplicates() secondary_works = self._matches[self._matches[ constants.LABEL_FIELDNAME] == secondary_label][ cols].drop_duplicates() for index, (work1, siglum1) in primary_works.iterrows(): text1 = self._get_text(self._corpus.get_witness(work1, siglum1)) label1 = '{}_{}'.format(work1, siglum1) for index, (work2, siglum2) in secondary_works.iterrows(): text2 = self._get_text(self._corpus.get_witness( work2, siglum2)) label2 = '{}_{}'.format(work2, siglum2) self._generate_sequences_for_texts(label1, text1, label2, text2, ngrams)
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Generates aligned sequences between each witness labelled `primary_label` and each witness labelled `secondary_label`, based around `ngrams`. :param primary_label: label for one side of the pairs of witnesses to align :type primary_label: `str` :param secondary_label: label for the other side of the pairs of witnesses to align :type secondary_label: `str` :param ngrams: n-grams to base sequences off :type ngrams: `list` of `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/sequence.py#L151-L181
train
48,403
ajenhl/tacl
tacl/sequence.py
SequenceReport._generate_sequences_for_ngram
def _generate_sequences_for_ngram(self, t1, t2, ngram, covered_spans): """Generates aligned sequences for the texts `t1` and `t2`, based around `ngram`. Does not generate sequences that occur within `covered_spans`. :param t1: text content of first witness :type t1: `str` :param t2: text content of second witness :type t2: `str` :param ngram: n-gram to base sequences on :type ngram: `str` :param covered_spans: lists of start and end indices for parts of the texts already covered by a sequence :type covered_spans: `list` of two `list`s of 2-`tuple` of `int` """ self._logger.debug('Generating sequences for n-gram "{}"'.format( ngram)) pattern = re.compile(re.escape(ngram)) context_length = len(ngram) t1_spans = [match.span() for match in pattern.finditer(t1)] t2_spans = [match.span() for match in pattern.finditer(t2)] sequences = [] self._logger.debug(t1) for t1_span in t1_spans: for t2_span in t2_spans: if self._is_inside(t1_span, t2_span, covered_spans): self._logger.debug( 'Skipping match due to existing coverage') continue sequence = self._generate_sequence( t1, t1_span, t2, t2_span, context_length, covered_spans) if sequence: sequences.append(sequence) return sequences
python
def _generate_sequences_for_ngram(self, t1, t2, ngram, covered_spans): """Generates aligned sequences for the texts `t1` and `t2`, based around `ngram`. Does not generate sequences that occur within `covered_spans`. :param t1: text content of first witness :type t1: `str` :param t2: text content of second witness :type t2: `str` :param ngram: n-gram to base sequences on :type ngram: `str` :param covered_spans: lists of start and end indices for parts of the texts already covered by a sequence :type covered_spans: `list` of two `list`s of 2-`tuple` of `int` """ self._logger.debug('Generating sequences for n-gram "{}"'.format( ngram)) pattern = re.compile(re.escape(ngram)) context_length = len(ngram) t1_spans = [match.span() for match in pattern.finditer(t1)] t2_spans = [match.span() for match in pattern.finditer(t2)] sequences = [] self._logger.debug(t1) for t1_span in t1_spans: for t2_span in t2_spans: if self._is_inside(t1_span, t2_span, covered_spans): self._logger.debug( 'Skipping match due to existing coverage') continue sequence = self._generate_sequence( t1, t1_span, t2, t2_span, context_length, covered_spans) if sequence: sequences.append(sequence) return sequences
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/sequence.py#L183-L218
train
48,404
ajenhl/tacl
tacl/sequence.py
SequenceReport._generate_sequences_for_texts
def _generate_sequences_for_texts(self, l1, t1, l2, t2, ngrams): """Generates and outputs aligned sequences for the texts `t1` and `t2` from `ngrams`. :param l1: label of first witness :type l1: `str` :param t1: text content of first witness :type t1: `str` :param l2: label of second witness :type l2: `str` :param t2: text content of second witness :type t2: `str` :param ngrams: n-grams to base sequences on :type ngrams: `list` of `str` """ # self._subsitutes is gradually populated as each text is # processed, so this needs to be regenerated each time. self._reverse_substitutes = dict((v, k) for k, v in self._substitutes.items()) sequences = [] # Keep track of spans within each text that have been covered # by an aligned sequence, to ensure that they aren't reported # more than once. The first sub-list contains span indices for # text t1, the second for t2. covered_spans = [[], []] for ngram in ngrams: sequences.extend(self._generate_sequences_for_ngram( t1, t2, ngram, covered_spans)) if sequences: sequences.sort(key=lambda x: x.start_index) context = {'l1': l1, 'l2': l2, 'sequences': sequences} report_name = '{}-{}.html'.format(l1, l2) os.makedirs(self._output_dir, exist_ok=True) self._write(context, self._output_dir, report_name)
python
def _generate_sequences_for_texts(self, l1, t1, l2, t2, ngrams): """Generates and outputs aligned sequences for the texts `t1` and `t2` from `ngrams`. :param l1: label of first witness :type l1: `str` :param t1: text content of first witness :type t1: `str` :param l2: label of second witness :type l2: `str` :param t2: text content of second witness :type t2: `str` :param ngrams: n-grams to base sequences on :type ngrams: `list` of `str` """ # self._subsitutes is gradually populated as each text is # processed, so this needs to be regenerated each time. self._reverse_substitutes = dict((v, k) for k, v in self._substitutes.items()) sequences = [] # Keep track of spans within each text that have been covered # by an aligned sequence, to ensure that they aren't reported # more than once. The first sub-list contains span indices for # text t1, the second for t2. covered_spans = [[], []] for ngram in ngrams: sequences.extend(self._generate_sequences_for_ngram( t1, t2, ngram, covered_spans)) if sequences: sequences.sort(key=lambda x: x.start_index) context = {'l1': l1, 'l2': l2, 'sequences': sequences} report_name = '{}-{}.html'.format(l1, l2) os.makedirs(self._output_dir, exist_ok=True) self._write(context, self._output_dir, report_name)
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Generates and outputs aligned sequences for the texts `t1` and `t2` from `ngrams`. :param l1: label of first witness :type l1: `str` :param t1: text content of first witness :type t1: `str` :param l2: label of second witness :type l2: `str` :param t2: text content of second witness :type t2: `str` :param ngrams: n-grams to base sequences on :type ngrams: `list` of `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/sequence.py#L220-L254
train
48,405
ajenhl/tacl
tacl/sequence.py
SequenceReport._get_text
def _get_text(self, text): """Returns the text content of `text`, with all multi-character tokens replaced with a single character. Substitutions are recorded in self._substitutes. :param text: text to get content from :type text: `Text` :rtype: `str` """ tokens = text.get_tokens() for i, token in enumerate(tokens): if len(token) > 1: char = chr(self._char_code) substitute = self._substitutes.setdefault(token, char) if substitute == char: self._char_code += 1 tokens[i] = substitute return self._tokenizer.joiner.join(tokens)
python
def _get_text(self, text): """Returns the text content of `text`, with all multi-character tokens replaced with a single character. Substitutions are recorded in self._substitutes. :param text: text to get content from :type text: `Text` :rtype: `str` """ tokens = text.get_tokens() for i, token in enumerate(tokens): if len(token) > 1: char = chr(self._char_code) substitute = self._substitutes.setdefault(token, char) if substitute == char: self._char_code += 1 tokens[i] = substitute return self._tokenizer.joiner.join(tokens)
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Returns the text content of `text`, with all multi-character tokens replaced with a single character. Substitutions are recorded in self._substitutes. :param text: text to get content from :type text: `Text` :rtype: `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/sequence.py#L256-L274
train
48,406
ajenhl/tacl
tacl/sequence.py
SequenceReport._get_text_sequence
def _get_text_sequence(self, text, span, context_length): """Returns the subset of `text` encompassed by `span`, plus `context_length` characters before and after. :param text: text to extract the sequence from :type text: `str` :param span: start and end indices within `text` :type span: 2-`tuple` of `int` :param context_length: length of context on either side of `span` to include in the extract :type context_length: `int` """ start = max(0, span[0] - context_length) end = min(len(text), span[1] + context_length) return text[start:end], (start, end)
python
def _get_text_sequence(self, text, span, context_length): """Returns the subset of `text` encompassed by `span`, plus `context_length` characters before and after. :param text: text to extract the sequence from :type text: `str` :param span: start and end indices within `text` :type span: 2-`tuple` of `int` :param context_length: length of context on either side of `span` to include in the extract :type context_length: `int` """ start = max(0, span[0] - context_length) end = min(len(text), span[1] + context_length) return text[start:end], (start, end)
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Returns the subset of `text` encompassed by `span`, plus `context_length` characters before and after. :param text: text to extract the sequence from :type text: `str` :param span: start and end indices within `text` :type span: 2-`tuple` of `int` :param context_length: length of context on either side of `span` to include in the extract :type context_length: `int`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/sequence.py#L276-L291
train
48,407
ajenhl/tacl
tacl/sequence.py
SequenceReport._is_inside
def _is_inside(self, span1, span2, covered_spans): """Returns True if both `span1` and `span2` fall within `covered_spans`. :param span1: start and end indices of a span :type span1: 2-`tuple` of `int` :param span2: start and end indices of a span :type span2: 2-`tuple` of `int` :param covered_spans: lists of start and end indices for parts of the texts already covered by a sequence :type covered_spans: `list` of two `list`s of 2-`tuple` of `int` :rtype: `bool` """ if self._is_span_inside(span1, covered_spans[0]) and \ self._is_span_inside(span2, covered_spans[1]): return True return False
python
def _is_inside(self, span1, span2, covered_spans): """Returns True if both `span1` and `span2` fall within `covered_spans`. :param span1: start and end indices of a span :type span1: 2-`tuple` of `int` :param span2: start and end indices of a span :type span2: 2-`tuple` of `int` :param covered_spans: lists of start and end indices for parts of the texts already covered by a sequence :type covered_spans: `list` of two `list`s of 2-`tuple` of `int` :rtype: `bool` """ if self._is_span_inside(span1, covered_spans[0]) and \ self._is_span_inside(span2, covered_spans[1]): return True return False
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Returns True if both `span1` and `span2` fall within `covered_spans`. :param span1: start and end indices of a span :type span1: 2-`tuple` of `int` :param span2: start and end indices of a span :type span2: 2-`tuple` of `int` :param covered_spans: lists of start and end indices for parts of the texts already covered by a sequence :type covered_spans: `list` of two `list`s of 2-`tuple` of `int` :rtype: `bool`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/sequence.py#L293-L310
train
48,408
ajenhl/tacl
tacl/sequence.py
SequenceReport._is_span_inside
def _is_span_inside(self, span, covered_spans): """Returns True if `span` falls within `covered_spans`. :param span: start and end indices of a span :type span: 2-`tuple` of `int` :param covered_spans: list of start and end indices for parts of the text already covered by a sequence :type covered_spans: `list` of 2-`tuple` of `int` :rtype: `bool` """ start = span[0] end = span[1] for c_start, c_end in covered_spans: if start >= c_start and end <= c_end: return True return False
python
def _is_span_inside(self, span, covered_spans): """Returns True if `span` falls within `covered_spans`. :param span: start and end indices of a span :type span: 2-`tuple` of `int` :param covered_spans: list of start and end indices for parts of the text already covered by a sequence :type covered_spans: `list` of 2-`tuple` of `int` :rtype: `bool` """ start = span[0] end = span[1] for c_start, c_end in covered_spans: if start >= c_start and end <= c_end: return True return False
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/sequence.py#L312-L328
train
48,409
ajenhl/tacl
tacl/cli/utils.py
add_corpus_arguments
def add_corpus_arguments(parser): """Adds common arguments for commands making use of a corpus to `parser`.""" add_tokenizer_argument(parser) parser.add_argument('corpus', help=constants.DB_CORPUS_HELP, metavar='CORPUS')
python
def add_corpus_arguments(parser): """Adds common arguments for commands making use of a corpus to `parser`.""" add_tokenizer_argument(parser) parser.add_argument('corpus', help=constants.DB_CORPUS_HELP, metavar='CORPUS')
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/cli/utils.py#L18-L23
train
48,410
ajenhl/tacl
tacl/cli/utils.py
add_db_arguments
def add_db_arguments(parser, db_option=False): """Adds common arguments for the database sub-commands to `parser`. `db_option` provides a means to work around https://bugs.python.org/issue9338 whereby a positional argument that follows an optional argument with nargs='+' will not be recognised. When `db_optional` is True, create the database argument as a required optional argument, rather than a positional argument. """ parser.add_argument('-m', '--memory', action='store_true', help=constants.DB_MEMORY_HELP) parser.add_argument('-r', '--ram', default=3, help=constants.DB_RAM_HELP, type=int) if db_option: parser.add_argument('-d', '--db', help=constants.DB_DATABASE_HELP, metavar='DATABASE', required=True) else: parser.add_argument('db', help=constants.DB_DATABASE_HELP, metavar='DATABASE')
python
def add_db_arguments(parser, db_option=False): """Adds common arguments for the database sub-commands to `parser`. `db_option` provides a means to work around https://bugs.python.org/issue9338 whereby a positional argument that follows an optional argument with nargs='+' will not be recognised. When `db_optional` is True, create the database argument as a required optional argument, rather than a positional argument. """ parser.add_argument('-m', '--memory', action='store_true', help=constants.DB_MEMORY_HELP) parser.add_argument('-r', '--ram', default=3, help=constants.DB_RAM_HELP, type=int) if db_option: parser.add_argument('-d', '--db', help=constants.DB_DATABASE_HELP, metavar='DATABASE', required=True) else: parser.add_argument('db', help=constants.DB_DATABASE_HELP, metavar='DATABASE')
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/cli/utils.py#L26-L47
train
48,411
ajenhl/tacl
tacl/cli/utils.py
add_supplied_query_arguments
def add_supplied_query_arguments(parser): """Adds common arguments for supplied query sub-commands to `parser`.""" parser.add_argument('-l', '--labels', help=constants.SUPPLIED_LABELS_HELP, nargs='+', required=True) parser.add_argument('-s', '--supplied', help=constants.SUPPLIED_RESULTS_HELP, metavar='RESULTS', nargs='+', required=True)
python
def add_supplied_query_arguments(parser): """Adds common arguments for supplied query sub-commands to `parser`.""" parser.add_argument('-l', '--labels', help=constants.SUPPLIED_LABELS_HELP, nargs='+', required=True) parser.add_argument('-s', '--supplied', help=constants.SUPPLIED_RESULTS_HELP, metavar='RESULTS', nargs='+', required=True)
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/cli/utils.py#L56-L63
train
48,412
ajenhl/tacl
tacl/cli/utils.py
configure_logging
def configure_logging(verbose, logger): """Configures the logging used.""" if not verbose: log_level = logging.WARNING elif verbose == 1: log_level = logging.INFO else: log_level = logging.DEBUG logger.setLevel(log_level) ch = colorlog.StreamHandler() ch.setLevel(log_level) formatter = colorlog.ColoredFormatter( '%(log_color)s%(asctime)s %(name)s %(levelname)s: %(message)s') ch.setFormatter(formatter) logger.addHandler(ch)
python
def configure_logging(verbose, logger): """Configures the logging used.""" if not verbose: log_level = logging.WARNING elif verbose == 1: log_level = logging.INFO else: log_level = logging.DEBUG logger.setLevel(log_level) ch = colorlog.StreamHandler() ch.setLevel(log_level) formatter = colorlog.ColoredFormatter( '%(log_color)s%(asctime)s %(name)s %(levelname)s: %(message)s') ch.setFormatter(formatter) logger.addHandler(ch)
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/cli/utils.py#L73-L87
train
48,413
ajenhl/tacl
tacl/cli/utils.py
get_catalogue
def get_catalogue(args): """Returns a `tacl.Catalogue`.""" catalogue = tacl.Catalogue() catalogue.load(args.catalogue) return catalogue
python
def get_catalogue(args): """Returns a `tacl.Catalogue`.""" catalogue = tacl.Catalogue() catalogue.load(args.catalogue) return catalogue
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/cli/utils.py#L90-L94
train
48,414
ajenhl/tacl
tacl/cli/utils.py
get_corpus
def get_corpus(args): """Returns a `tacl.Corpus`.""" tokenizer = get_tokenizer(args) return tacl.Corpus(args.corpus, tokenizer)
python
def get_corpus(args): """Returns a `tacl.Corpus`.""" tokenizer = get_tokenizer(args) return tacl.Corpus(args.corpus, tokenizer)
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/cli/utils.py#L97-L100
train
48,415
ajenhl/tacl
tacl/cli/utils.py
get_data_store
def get_data_store(args): """Returns a `tacl.DataStore`.""" return tacl.DataStore(args.db, args.memory, args.ram)
python
def get_data_store(args): """Returns a `tacl.DataStore`.""" return tacl.DataStore(args.db, args.memory, args.ram)
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/cli/utils.py#L103-L105
train
48,416
ajenhl/tacl
tacl/cli/utils.py
get_ngrams
def get_ngrams(path): """Returns a list of n-grams read from the file at `path`.""" with open(path, encoding='utf-8') as fh: ngrams = [ngram.strip() for ngram in fh.readlines()] return ngrams
python
def get_ngrams(path): """Returns a list of n-grams read from the file at `path`.""" with open(path, encoding='utf-8') as fh: ngrams = [ngram.strip() for ngram in fh.readlines()] return ngrams
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Returns a list of n-grams read from the file at `path`.
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/cli/utils.py#L108-L112
train
48,417
ajenhl/tacl
tacl/text.py
Text.excise
def excise(self, ngrams, replacement): """Returns the token content of this text with every occurrence of each n-gram in `ngrams` replaced with `replacement`. The replacing is performed on each n-gram by descending order of length. :param ngrams: n-grams to be replaced :type ngrams: `list` of `str` :param replacement: replacement string :type replacement: `str` :rtype: `str` """ content = self.get_token_content() ngrams.sort(key=len, reverse=True) for ngram in ngrams: content = content.replace(ngram, replacement) return content
python
def excise(self, ngrams, replacement): """Returns the token content of this text with every occurrence of each n-gram in `ngrams` replaced with `replacement`. The replacing is performed on each n-gram by descending order of length. :param ngrams: n-grams to be replaced :type ngrams: `list` of `str` :param replacement: replacement string :type replacement: `str` :rtype: `str` """ content = self.get_token_content() ngrams.sort(key=len, reverse=True) for ngram in ngrams: content = content.replace(ngram, replacement) return content
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/text.py#L22-L40
train
48,418
ajenhl/tacl
tacl/text.py
Text._ngrams
def _ngrams(self, sequence, degree): """Returns the n-grams generated from `sequence`. Based on the ngrams function from the Natural Language Toolkit. Each n-gram in the returned list is a string with whitespace removed. :param sequence: the source data to be converted into n-grams :type sequence: sequence :param degree: the degree of the n-grams :type degree: `int` :rtype: `list` of `str` """ count = max(0, len(sequence) - degree + 1) # The extra split and join are due to having to handle # whitespace within a CBETA token (eg, [(禾*尤)\n/上/日]). return [self._tokenizer.joiner.join( self._tokenizer.joiner.join(sequence[i:i+degree]).split()) for i in range(count)]
python
def _ngrams(self, sequence, degree): """Returns the n-grams generated from `sequence`. Based on the ngrams function from the Natural Language Toolkit. Each n-gram in the returned list is a string with whitespace removed. :param sequence: the source data to be converted into n-grams :type sequence: sequence :param degree: the degree of the n-grams :type degree: `int` :rtype: `list` of `str` """ count = max(0, len(sequence) - degree + 1) # The extra split and join are due to having to handle # whitespace within a CBETA token (eg, [(禾*尤)\n/上/日]). return [self._tokenizer.joiner.join( self._tokenizer.joiner.join(sequence[i:i+degree]).split()) for i in range(count)]
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/text.py#L91-L112
train
48,419
ajenhl/tacl
tacl/text.py
FilteredWitnessText.get_filter_ngrams_pattern
def get_filter_ngrams_pattern(filter_ngrams): """Returns a compiled regular expression matching on any of the n-grams in `filter_ngrams`. :param filter_ngrams: n-grams to use in regular expression :type filter_ngrams: `list` of `str` :rtype: `_sre.SRE_Pattern` """ return re.compile('|'.join([re.escape(ngram) for ngram in filter_ngrams]))
python
def get_filter_ngrams_pattern(filter_ngrams): """Returns a compiled regular expression matching on any of the n-grams in `filter_ngrams`. :param filter_ngrams: n-grams to use in regular expression :type filter_ngrams: `list` of `str` :rtype: `_sre.SRE_Pattern` """ return re.compile('|'.join([re.escape(ngram) for ngram in filter_ngrams]))
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/text.py#L161-L171
train
48,420
peeringdb/django-peeringdb
django_peeringdb/client_adaptor/backend.py
Backend.set_relation_many_to_many
def set_relation_many_to_many(self, obj, field_name, objs): "Set a many-to-many field on an object" relation = getattr(obj, field_name) if hasattr(relation, 'set'): relation.set(objs) # Django 2.x else: setattr(obj, field_name, objs)
python
def set_relation_many_to_many(self, obj, field_name, objs): "Set a many-to-many field on an object" relation = getattr(obj, field_name) if hasattr(relation, 'set'): relation.set(objs) # Django 2.x else: setattr(obj, field_name, objs)
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2a32aae8a7e1c11ab6e5a873bb19619c641098c8
https://github.com/peeringdb/django-peeringdb/blob/2a32aae8a7e1c11ab6e5a873bb19619c641098c8/django_peeringdb/client_adaptor/backend.py#L136-L142
train
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peeringdb/django-peeringdb
django_peeringdb/client_adaptor/backend.py
Backend.detect_uniqueness_error
def detect_uniqueness_error(self, exc): """ Parse error, and if it describes any violations of a uniqueness constraint, return the corresponding fields, else None """ pattern = r"(\w+) with this (\w+) already exists" fields = [] if isinstance(exc, IntegrityError): return self._detect_integrity_error(exc) assert isinstance(exc, ValidationError), TypeError for name, err in exc.error_dict.items(): if re.search(pattern, str(err)): fields.append(name) return fields or None
python
def detect_uniqueness_error(self, exc): """ Parse error, and if it describes any violations of a uniqueness constraint, return the corresponding fields, else None """ pattern = r"(\w+) with this (\w+) already exists" fields = [] if isinstance(exc, IntegrityError): return self._detect_integrity_error(exc) assert isinstance(exc, ValidationError), TypeError for name, err in exc.error_dict.items(): if re.search(pattern, str(err)): fields.append(name) return fields or None
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2a32aae8a7e1c11ab6e5a873bb19619c641098c8
https://github.com/peeringdb/django-peeringdb/blob/2a32aae8a7e1c11ab6e5a873bb19619c641098c8/django_peeringdb/client_adaptor/backend.py#L173-L188
train
48,422
SuperCowPowers/chains
chains/links/tls_meta.py
TLSMeta.tls_meta_data
def tls_meta_data(self): """Pull out the TLS metadata for each flow in the input_stream""" # For each flow process the contents for flow in self.input_stream: # Just TCP for now if flow['protocol'] != 'TCP': continue # Client to Server if flow['direction'] == 'CTS': # Try to process the payload as a set of TLS records try: tls_records, bytes_consumed = dpkt.ssl.tls_multi_factory(flow['payload']) if bytes_consumed != len(flow['payload']): logger.warning('Incomplete TLS record at the end...') # Process the TLS records flow['tls'] = {'type':'TLS_CTS', 'data':{'tls_records': tls_records, 'uri':None, 'headers':None}} except (dpkt.dpkt.NeedData, dpkt.dpkt.UnpackError, dpkt.ssl.SSL3Exception): flow['tls'] = None # Server to Client else: try: tls_records, bytes_consumed = dpkt.ssl.tls_multi_factory(flow['payload']) if bytes_consumed != len(flow['payload']): logger.warning('Incomplete TLS record at the end...') # Process the TLS records flow['tls'] = {'type':'TLS_STC', 'data':{'tls_records': tls_records, 'uri':None, 'headers':None}} except (dpkt.dpkt.NeedData, dpkt.dpkt.UnpackError, dpkt.ssl.SSL3Exception): flow['tls'] = None # All done yield flow
python
def tls_meta_data(self): """Pull out the TLS metadata for each flow in the input_stream""" # For each flow process the contents for flow in self.input_stream: # Just TCP for now if flow['protocol'] != 'TCP': continue # Client to Server if flow['direction'] == 'CTS': # Try to process the payload as a set of TLS records try: tls_records, bytes_consumed = dpkt.ssl.tls_multi_factory(flow['payload']) if bytes_consumed != len(flow['payload']): logger.warning('Incomplete TLS record at the end...') # Process the TLS records flow['tls'] = {'type':'TLS_CTS', 'data':{'tls_records': tls_records, 'uri':None, 'headers':None}} except (dpkt.dpkt.NeedData, dpkt.dpkt.UnpackError, dpkt.ssl.SSL3Exception): flow['tls'] = None # Server to Client else: try: tls_records, bytes_consumed = dpkt.ssl.tls_multi_factory(flow['payload']) if bytes_consumed != len(flow['payload']): logger.warning('Incomplete TLS record at the end...') # Process the TLS records flow['tls'] = {'type':'TLS_STC', 'data':{'tls_records': tls_records, 'uri':None, 'headers':None}} except (dpkt.dpkt.NeedData, dpkt.dpkt.UnpackError, dpkt.ssl.SSL3Exception): flow['tls'] = None # All done yield flow
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b0227847b0c43083b456f0bae52daee0b62a3e03
https://github.com/SuperCowPowers/chains/blob/b0227847b0c43083b456f0bae52daee0b62a3e03/chains/links/tls_meta.py#L22-L59
train
48,423
SuperCowPowers/chains
chains/utils/data_utils.py
make_dict
def make_dict(obj): """This method creates a dictionary out of a non-builtin object""" # Recursion base case if is_builtin(obj) or isinstance(obj, OrderedDict): return obj output_dict = {} for key in dir(obj): if not key.startswith('__') and not callable(getattr(obj, key)): attr = getattr(obj, key) if isinstance(attr, list): output_dict[key] = [] for item in attr: output_dict[key].append(make_dict(item)) else: output_dict[key] = make_dict(attr) # All done return output_dict
python
def make_dict(obj): """This method creates a dictionary out of a non-builtin object""" # Recursion base case if is_builtin(obj) or isinstance(obj, OrderedDict): return obj output_dict = {} for key in dir(obj): if not key.startswith('__') and not callable(getattr(obj, key)): attr = getattr(obj, key) if isinstance(attr, list): output_dict[key] = [] for item in attr: output_dict[key].append(make_dict(item)) else: output_dict[key] = make_dict(attr) # All done return output_dict
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b0227847b0c43083b456f0bae52daee0b62a3e03
https://github.com/SuperCowPowers/chains/blob/b0227847b0c43083b456f0bae52daee0b62a3e03/chains/utils/data_utils.py#L9-L28
train
48,424
SuperCowPowers/chains
chains/utils/data_utils.py
get_value
def get_value(data, key): """Follow the dot notation to get the proper field, then perform the action Args: data: the data as a dictionary (required to be a dictionary) key: the key (as dot notation) into the data that gives the field (IP.src) Returns: the value of the field(subfield) if it exist, otherwise None """ ref = data try: for subkey in key.split('.'): if isinstance(ref, dict): ref = ref[subkey] else: print('CRITICAL: Cannot use subkey %s on non-dictionary element' % subkey) return None return ref # In general KeyErrors are expected except KeyError: return None
python
def get_value(data, key): """Follow the dot notation to get the proper field, then perform the action Args: data: the data as a dictionary (required to be a dictionary) key: the key (as dot notation) into the data that gives the field (IP.src) Returns: the value of the field(subfield) if it exist, otherwise None """ ref = data try: for subkey in key.split('.'): if isinstance(ref, dict): ref = ref[subkey] else: print('CRITICAL: Cannot use subkey %s on non-dictionary element' % subkey) return None return ref # In general KeyErrors are expected except KeyError: return None
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Follow the dot notation to get the proper field, then perform the action Args: data: the data as a dictionary (required to be a dictionary) key: the key (as dot notation) into the data that gives the field (IP.src) Returns: the value of the field(subfield) if it exist, otherwise None
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b0227847b0c43083b456f0bae52daee0b62a3e03
https://github.com/SuperCowPowers/chains/blob/b0227847b0c43083b456f0bae52daee0b62a3e03/chains/utils/data_utils.py#L33-L55
train
48,425
ajenhl/tacl
tacl/statistics_report.py
StatisticsReport.csv
def csv(self, fh): """Writes the report data to `fh` in CSV format and returns it. :param fh: file to write data to :type fh: file object :rtype: file object """ self._stats.to_csv(fh, encoding='utf-8', index=False) return fh
python
def csv(self, fh): """Writes the report data to `fh` in CSV format and returns it. :param fh: file to write data to :type fh: file object :rtype: file object """ self._stats.to_csv(fh, encoding='utf-8', index=False) return fh
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Writes the report data to `fh` in CSV format and returns it. :param fh: file to write data to :type fh: file object :rtype: file object
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/statistics_report.py#L19-L28
train
48,426
ajenhl/tacl
tacl/statistics_report.py
StatisticsReport.generate_statistics
def generate_statistics(self): """Replaces result rows with summary statistics about the results. These statistics give the filename, total matching tokens, percentage of matching tokens and label for each witness in the results. """ matches = self._matches witness_fields = [constants.WORK_FIELDNAME, constants.SIGLUM_FIELDNAME, constants.LABEL_FIELDNAME] witnesses = matches[witness_fields].drop_duplicates() rows = [] for index, (work, siglum, label) in witnesses.iterrows(): witness = self._corpus.get_witness(work, siglum) witness_matches = matches[ (matches[constants.WORK_FIELDNAME] == work) & (matches[constants.SIGLUM_FIELDNAME] == siglum)] total_count, matching_count = self._process_witness( witness, witness_matches) percentage = matching_count / total_count * 100 rows.append({constants.WORK_FIELDNAME: work, constants.SIGLUM_FIELDNAME: siglum, constants.COUNT_TOKENS_FIELDNAME: matching_count, constants.TOTAL_TOKENS_FIELDNAME: total_count, constants.PERCENTAGE_FIELDNAME: percentage, constants.LABEL_FIELDNAME: label}) self._stats = pd.DataFrame( rows, columns=constants.STATISTICS_FIELDNAMES)
python
def generate_statistics(self): """Replaces result rows with summary statistics about the results. These statistics give the filename, total matching tokens, percentage of matching tokens and label for each witness in the results. """ matches = self._matches witness_fields = [constants.WORK_FIELDNAME, constants.SIGLUM_FIELDNAME, constants.LABEL_FIELDNAME] witnesses = matches[witness_fields].drop_duplicates() rows = [] for index, (work, siglum, label) in witnesses.iterrows(): witness = self._corpus.get_witness(work, siglum) witness_matches = matches[ (matches[constants.WORK_FIELDNAME] == work) & (matches[constants.SIGLUM_FIELDNAME] == siglum)] total_count, matching_count = self._process_witness( witness, witness_matches) percentage = matching_count / total_count * 100 rows.append({constants.WORK_FIELDNAME: work, constants.SIGLUM_FIELDNAME: siglum, constants.COUNT_TOKENS_FIELDNAME: matching_count, constants.TOTAL_TOKENS_FIELDNAME: total_count, constants.PERCENTAGE_FIELDNAME: percentage, constants.LABEL_FIELDNAME: label}) self._stats = pd.DataFrame( rows, columns=constants.STATISTICS_FIELDNAMES)
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Replaces result rows with summary statistics about the results. These statistics give the filename, total matching tokens, percentage of matching tokens and label for each witness in the results.
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/statistics_report.py#L30-L58
train
48,427
ajenhl/tacl
tacl/statistics_report.py
StatisticsReport._generate_text_from_slices
def _generate_text_from_slices(self, full_text, slices): """Return a single string consisting of the parts specified in `slices` joined together by the tokenizer's joining string. :param full_text: the text to be sliced :type full_text: `str` :param slices: list of slice indices to apply to `full_text` :type slices: `list` of `list`\s :rtype: `str` """ sliced_text = [] for start, end in slices: sliced_text.append(full_text[start:end]) return self._tokenizer.joiner.join(sliced_text)
python
def _generate_text_from_slices(self, full_text, slices): """Return a single string consisting of the parts specified in `slices` joined together by the tokenizer's joining string. :param full_text: the text to be sliced :type full_text: `str` :param slices: list of slice indices to apply to `full_text` :type slices: `list` of `list`\s :rtype: `str` """ sliced_text = [] for start, end in slices: sliced_text.append(full_text[start:end]) return self._tokenizer.joiner.join(sliced_text)
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Return a single string consisting of the parts specified in `slices` joined together by the tokenizer's joining string. :param full_text: the text to be sliced :type full_text: `str` :param slices: list of slice indices to apply to `full_text` :type slices: `list` of `list`\s :rtype: `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/statistics_report.py#L60-L74
train
48,428
ajenhl/tacl
tacl/statistics_report.py
StatisticsReport._merge_slices
def _merge_slices(match_slices): """Return a list of slice indices lists derived from `match_slices` with no overlaps.""" # Sort by earliest range, then by largest range. match_slices.sort(key=lambda x: (x[0], -x[1])) merged_slices = [match_slices.pop(0)] for slice_indices in match_slices: last_end = merged_slices[-1][1] if slice_indices[0] <= last_end: if slice_indices[1] > last_end: merged_slices[-1][1] = slice_indices[1] else: merged_slices.append(slice_indices) return merged_slices
python
def _merge_slices(match_slices): """Return a list of slice indices lists derived from `match_slices` with no overlaps.""" # Sort by earliest range, then by largest range. match_slices.sort(key=lambda x: (x[0], -x[1])) merged_slices = [match_slices.pop(0)] for slice_indices in match_slices: last_end = merged_slices[-1][1] if slice_indices[0] <= last_end: if slice_indices[1] > last_end: merged_slices[-1][1] = slice_indices[1] else: merged_slices.append(slice_indices) return merged_slices
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Return a list of slice indices lists derived from `match_slices` with no overlaps.
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/statistics_report.py#L77-L90
train
48,429
ajenhl/tacl
tacl/statistics_report.py
StatisticsReport._process_witness
def _process_witness(self, witness, matches): """Return the counts of total tokens and matching tokens in `witness`. :param witness: witness text :type witness: `tacl.WitnessText` :param matches: n-gram matches :type matches: `pandas.DataFrame` :rtype: `tuple` of `int` """ # In order to provide a correct count of matched tokens, # avoiding the twin dangers of counting the same token # multiple times due to being part of multiple n-grams (which # can happen even in reduced results) and not counting tokens # due to an n-gram overlapping with itself or another n-gram, # a bit of work is required. # # Using regular expressions, get the slice indices for all # matches (including overlapping ones) for all matching # n-grams. Merge these slices together (without overlap) and # create a Text using that text, which can then be tokenised # and the tokens counted. tokens = witness.get_tokens() full_text = witness.get_token_content() fields = [constants.NGRAM_FIELDNAME, constants.SIZE_FIELDNAME] match_slices = [] for index, (ngram, size) in matches[fields].iterrows(): pattern = re.compile(re.escape(ngram)) # Because the same n-gram may overlap itself ("heh" in the # string "heheh"), re.findall cannot be used. start = 0 while True: match = pattern.search(full_text, start) if match is None: break match_slices.append([match.start(), match.end()]) start = match.start() + 1 merged_slices = self._merge_slices(match_slices) match_content = self._generate_text_from_slices( full_text, merged_slices) match_text = Text(match_content, self._tokenizer) return len(tokens), len(match_text.get_tokens())
python
def _process_witness(self, witness, matches): """Return the counts of total tokens and matching tokens in `witness`. :param witness: witness text :type witness: `tacl.WitnessText` :param matches: n-gram matches :type matches: `pandas.DataFrame` :rtype: `tuple` of `int` """ # In order to provide a correct count of matched tokens, # avoiding the twin dangers of counting the same token # multiple times due to being part of multiple n-grams (which # can happen even in reduced results) and not counting tokens # due to an n-gram overlapping with itself or another n-gram, # a bit of work is required. # # Using regular expressions, get the slice indices for all # matches (including overlapping ones) for all matching # n-grams. Merge these slices together (without overlap) and # create a Text using that text, which can then be tokenised # and the tokens counted. tokens = witness.get_tokens() full_text = witness.get_token_content() fields = [constants.NGRAM_FIELDNAME, constants.SIZE_FIELDNAME] match_slices = [] for index, (ngram, size) in matches[fields].iterrows(): pattern = re.compile(re.escape(ngram)) # Because the same n-gram may overlap itself ("heh" in the # string "heheh"), re.findall cannot be used. start = 0 while True: match = pattern.search(full_text, start) if match is None: break match_slices.append([match.start(), match.end()]) start = match.start() + 1 merged_slices = self._merge_slices(match_slices) match_content = self._generate_text_from_slices( full_text, merged_slices) match_text = Text(match_content, self._tokenizer) return len(tokens), len(match_text.get_tokens())
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/statistics_report.py#L92-L133
train
48,430
ajenhl/tacl
tacl/stripper.py
Stripper.get_witnesses
def get_witnesses(self, source_tree): """Returns a list of all witnesses of variant readings in `source_tree` along with their XML ids. :param source_tree: XML tree of source document :type source_tree: `etree._ElementTree` :rtype: `list` of `tuple` """ witnesses = [] witness_elements = source_tree.xpath( '/tei:*/tei:teiHeader/tei:fileDesc/tei:sourceDesc/' 'tei:listWit/tei:witness', namespaces=constants.NAMESPACES) for witness_element in witness_elements: witnesses.append((witness_element.text, witness_element.get(constants.XML + 'id'))) if not witnesses: witnesses = [(constants.BASE_WITNESS, constants.BASE_WITNESS_ID)] return witnesses
python
def get_witnesses(self, source_tree): """Returns a list of all witnesses of variant readings in `source_tree` along with their XML ids. :param source_tree: XML tree of source document :type source_tree: `etree._ElementTree` :rtype: `list` of `tuple` """ witnesses = [] witness_elements = source_tree.xpath( '/tei:*/tei:teiHeader/tei:fileDesc/tei:sourceDesc/' 'tei:listWit/tei:witness', namespaces=constants.NAMESPACES) for witness_element in witness_elements: witnesses.append((witness_element.text, witness_element.get(constants.XML + 'id'))) if not witnesses: witnesses = [(constants.BASE_WITNESS, constants.BASE_WITNESS_ID)] return witnesses
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Returns a list of all witnesses of variant readings in `source_tree` along with their XML ids. :param source_tree: XML tree of source document :type source_tree: `etree._ElementTree` :rtype: `list` of `tuple`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/stripper.py#L31-L49
train
48,431
SuperCowPowers/chains
examples/tag_example.py
run
def run(iface_name=None, bpf=None, summary=None, max_packets=50): """Run the Simple Packet Printer Example""" # Create the classes streamer = packet_streamer.PacketStreamer(iface_name=iface_name, bpf=bpf, max_packets=max_packets) meta = packet_meta.PacketMeta() rdns = reverse_dns.ReverseDNS() tags = packet_tags.PacketTags() tmeta = transport_meta.TransportMeta() printer = packet_summary.PacketSummary() # Set up the chain meta.link(streamer) rdns.link(meta) tags.link(rdns) tmeta.link(tags) printer.link(tmeta) # Pull the chain printer.pull()
python
def run(iface_name=None, bpf=None, summary=None, max_packets=50): """Run the Simple Packet Printer Example""" # Create the classes streamer = packet_streamer.PacketStreamer(iface_name=iface_name, bpf=bpf, max_packets=max_packets) meta = packet_meta.PacketMeta() rdns = reverse_dns.ReverseDNS() tags = packet_tags.PacketTags() tmeta = transport_meta.TransportMeta() printer = packet_summary.PacketSummary() # Set up the chain meta.link(streamer) rdns.link(meta) tags.link(rdns) tmeta.link(tags) printer.link(tmeta) # Pull the chain printer.pull()
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Run the Simple Packet Printer Example
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b0227847b0c43083b456f0bae52daee0b62a3e03
https://github.com/SuperCowPowers/chains/blob/b0227847b0c43083b456f0bae52daee0b62a3e03/examples/tag_example.py#L10-L29
train
48,432
ajenhl/tacl
tacl/lifetime_report.py
LifetimeReport.generate
def generate(self, output_dir, catalogue, results, label): """Generates the report, writing it to `output_dir`.""" data = results.get_raw_data() labels = catalogue.ordered_labels ngrams = self._generate_results(output_dir, labels, data) ngram_table = self._generate_ngram_table(output_dir, labels, data) corpus_table = self._generate_corpus_table(labels, ngrams) context = {'corpus_table': corpus_table, 'focus_label': label, 'labels': labels, 'ngram_table': ngram_table, 'sep': os.sep} report_name = 'lifetime-{}.html'.format(label) self._write(context, output_dir, report_name)
python
def generate(self, output_dir, catalogue, results, label): """Generates the report, writing it to `output_dir`.""" data = results.get_raw_data() labels = catalogue.ordered_labels ngrams = self._generate_results(output_dir, labels, data) ngram_table = self._generate_ngram_table(output_dir, labels, data) corpus_table = self._generate_corpus_table(labels, ngrams) context = {'corpus_table': corpus_table, 'focus_label': label, 'labels': labels, 'ngram_table': ngram_table, 'sep': os.sep} report_name = 'lifetime-{}.html'.format(label) self._write(context, output_dir, report_name)
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/lifetime_report.py#L30-L40
train
48,433
ajenhl/tacl
tacl/lifetime_report.py
LifetimeReport._generate_corpus_table
def _generate_corpus_table(self, labels, ngrams): """Returns an HTML table containing data on each corpus' n-grams.""" html = [] for label in labels: html.append(self._render_corpus_row(label, ngrams)) return '\n'.join(html)
python
def _generate_corpus_table(self, labels, ngrams): """Returns an HTML table containing data on each corpus' n-grams.""" html = [] for label in labels: html.append(self._render_corpus_row(label, ngrams)) return '\n'.join(html)
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/lifetime_report.py#L42-L47
train
48,434
ajenhl/tacl
tacl/lifetime_report.py
LifetimeReport._generate_ngram_table
def _generate_ngram_table(self, output_dir, labels, results): """Returns an HTML table containing data on each n-gram in `results`.""" html = [] grouped = results.groupby(constants.NGRAM_FIELDNAME) row_template = self._generate_ngram_row_template(labels) for name, group in grouped: html.append(self._render_ngram_row(name, group, row_template, labels)) return '\n'.join(html)
python
def _generate_ngram_table(self, output_dir, labels, results): """Returns an HTML table containing data on each n-gram in `results`.""" html = [] grouped = results.groupby(constants.NGRAM_FIELDNAME) row_template = self._generate_ngram_row_template(labels) for name, group in grouped: html.append(self._render_ngram_row(name, group, row_template, labels)) return '\n'.join(html)
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Returns an HTML table containing data on each n-gram in `results`.
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/lifetime_report.py#L49-L58
train
48,435
ajenhl/tacl
tacl/lifetime_report.py
LifetimeReport._generate_ngram_row_template
def _generate_ngram_row_template(self, labels): """Returns the HTML template for a row in the n-gram table.""" cells = ['<td>{ngram}</td>'] for label in labels: cells.append('<td>{{{}}}</td>'.format(label)) return '\n'.join(cells)
python
def _generate_ngram_row_template(self, labels): """Returns the HTML template for a row in the n-gram table.""" cells = ['<td>{ngram}</td>'] for label in labels: cells.append('<td>{{{}}}</td>'.format(label)) return '\n'.join(cells)
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Returns the HTML template for a row in the n-gram table.
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/lifetime_report.py#L60-L65
train
48,436
ajenhl/tacl
tacl/lifetime_report.py
LifetimeReport._generate_results
def _generate_results(self, output_dir, labels, results): """Creates multiple results files in `output_dir` based on `results`. For each label in `labels`, create three results file, containing those n-grams with that label that first occurred, only occurred, and last occurred in that label. """ ngrams = {} for idx, label in enumerate(labels): now_results = results[results[constants.LABEL_FIELDNAME] == label] earlier_labels = labels[:idx] earlier_ngrams = results[results[constants.LABEL_FIELDNAME].isin( earlier_labels)][constants.NGRAM_FIELDNAME].values later_labels = labels[idx + 1:] later_ngrams = results[results[constants.LABEL_FIELDNAME].isin( later_labels)][constants.NGRAM_FIELDNAME].values first_ngrams = [] only_ngrams = [] last_ngrams = [] for ngram in now_results[constants.NGRAM_FIELDNAME].unique(): if ngram in earlier_ngrams: if ngram not in later_ngrams: last_ngrams.append(ngram) elif ngram in later_ngrams: first_ngrams.append(ngram) else: only_ngrams.append(ngram) self._save_results(output_dir, label, now_results, first_ngrams, 'first') self._save_results(output_dir, label, now_results, only_ngrams, 'only') self._save_results(output_dir, label, now_results, last_ngrams, 'last') ngrams[label] = {'first': first_ngrams, 'last': last_ngrams, 'only': only_ngrams} return ngrams
python
def _generate_results(self, output_dir, labels, results): """Creates multiple results files in `output_dir` based on `results`. For each label in `labels`, create three results file, containing those n-grams with that label that first occurred, only occurred, and last occurred in that label. """ ngrams = {} for idx, label in enumerate(labels): now_results = results[results[constants.LABEL_FIELDNAME] == label] earlier_labels = labels[:idx] earlier_ngrams = results[results[constants.LABEL_FIELDNAME].isin( earlier_labels)][constants.NGRAM_FIELDNAME].values later_labels = labels[idx + 1:] later_ngrams = results[results[constants.LABEL_FIELDNAME].isin( later_labels)][constants.NGRAM_FIELDNAME].values first_ngrams = [] only_ngrams = [] last_ngrams = [] for ngram in now_results[constants.NGRAM_FIELDNAME].unique(): if ngram in earlier_ngrams: if ngram not in later_ngrams: last_ngrams.append(ngram) elif ngram in later_ngrams: first_ngrams.append(ngram) else: only_ngrams.append(ngram) self._save_results(output_dir, label, now_results, first_ngrams, 'first') self._save_results(output_dir, label, now_results, only_ngrams, 'only') self._save_results(output_dir, label, now_results, last_ngrams, 'last') ngrams[label] = {'first': first_ngrams, 'last': last_ngrams, 'only': only_ngrams} return ngrams
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Creates multiple results files in `output_dir` based on `results`. For each label in `labels`, create three results file, containing those n-grams with that label that first occurred, only occurred, and last occurred in that label.
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/lifetime_report.py#L67-L103
train
48,437
ajenhl/tacl
tacl/lifetime_report.py
LifetimeReport._render_corpus_row
def _render_corpus_row(self, label, ngrams): """Returns the HTML for a corpus row.""" row = ('<tr>\n<td>{label}</td>\n<td>{first}</td>\n<td>{only}</td>\n' '<td>{last}</td>\n</tr>') cell_data = {'label': label} for period in ('first', 'only', 'last'): cell_data[period] = ', '.join(ngrams[label][period]) return row.format(**cell_data)
python
def _render_corpus_row(self, label, ngrams): """Returns the HTML for a corpus row.""" row = ('<tr>\n<td>{label}</td>\n<td>{first}</td>\n<td>{only}</td>\n' '<td>{last}</td>\n</tr>') cell_data = {'label': label} for period in ('first', 'only', 'last'): cell_data[period] = ', '.join(ngrams[label][period]) return row.format(**cell_data)
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Returns the HTML for a corpus row.
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/lifetime_report.py#L105-L112
train
48,438
ajenhl/tacl
tacl/lifetime_report.py
LifetimeReport._render_ngram_row
def _render_ngram_row(self, ngram, ngram_group, row_template, labels): """Returns the HTML for an n-gram row.""" cell_data = {'ngram': ngram} label_data = {} for label in labels: label_data[label] = [] work_grouped = ngram_group.groupby(constants.WORK_FIELDNAME) for work, group in work_grouped: min_count = group[constants.COUNT_FIELDNAME].min() max_count = group[constants.COUNT_FIELDNAME].max() if min_count == max_count: count = min_count else: count = '{}\N{EN DASH}{}'.format(min_count, max_count) label_data[group[constants.LABEL_FIELDNAME].iloc[0]].append( '{} ({})'.format(work, count)) for label, data in label_data.items(): label_data[label] = '; '.join(data) cell_data.update(label_data) html = row_template.format(**cell_data) return '<tr>\n{}\n</tr>'.format(html)
python
def _render_ngram_row(self, ngram, ngram_group, row_template, labels): """Returns the HTML for an n-gram row.""" cell_data = {'ngram': ngram} label_data = {} for label in labels: label_data[label] = [] work_grouped = ngram_group.groupby(constants.WORK_FIELDNAME) for work, group in work_grouped: min_count = group[constants.COUNT_FIELDNAME].min() max_count = group[constants.COUNT_FIELDNAME].max() if min_count == max_count: count = min_count else: count = '{}\N{EN DASH}{}'.format(min_count, max_count) label_data[group[constants.LABEL_FIELDNAME].iloc[0]].append( '{} ({})'.format(work, count)) for label, data in label_data.items(): label_data[label] = '; '.join(data) cell_data.update(label_data) html = row_template.format(**cell_data) return '<tr>\n{}\n</tr>'.format(html)
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Returns the HTML for an n-gram row.
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/lifetime_report.py#L114-L134
train
48,439
ajenhl/tacl
tacl/lifetime_report.py
LifetimeReport._save_results
def _save_results(self, output_dir, label, results, ngrams, type_label): """Saves `results` filtered by `label` and `ngram` to `output_dir`. :param output_dir: directory to save results to :type output_dir: `str` :param label: catalogue label of results, used in saved filename :type label: `str` :param results: results to filter and save :type results: `pandas.DataFrame` :param ngrams: n-grams to save from results :type ngrams: `list` of `str` :param type_label: name of type of results, used in saved filename :type type_label: `str` """ path = os.path.join(output_dir, '{}-{}.csv'.format(label, type_label)) results[results[constants.NGRAM_FIELDNAME].isin( ngrams)].to_csv(path, encoding='utf-8', float_format='%d', index=False)
python
def _save_results(self, output_dir, label, results, ngrams, type_label): """Saves `results` filtered by `label` and `ngram` to `output_dir`. :param output_dir: directory to save results to :type output_dir: `str` :param label: catalogue label of results, used in saved filename :type label: `str` :param results: results to filter and save :type results: `pandas.DataFrame` :param ngrams: n-grams to save from results :type ngrams: `list` of `str` :param type_label: name of type of results, used in saved filename :type type_label: `str` """ path = os.path.join(output_dir, '{}-{}.csv'.format(label, type_label)) results[results[constants.NGRAM_FIELDNAME].isin( ngrams)].to_csv(path, encoding='utf-8', float_format='%d', index=False)
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Saves `results` filtered by `label` and `ngram` to `output_dir`. :param output_dir: directory to save results to :type output_dir: `str` :param label: catalogue label of results, used in saved filename :type label: `str` :param results: results to filter and save :type results: `pandas.DataFrame` :param ngrams: n-grams to save from results :type ngrams: `list` of `str` :param type_label: name of type of results, used in saved filename :type type_label: `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/lifetime_report.py#L136-L154
train
48,440
SuperCowPowers/chains
chains/links/link.py
Link.link
def link(self, stream_instance): """Set my input stream""" if isinstance(stream_instance, collections.Iterable): self.input_stream = stream_instance elif getattr(stream_instance, 'output_stream', None): self.input_stream = stream_instance.output_stream else: raise RuntimeError('Calling link() with unknown instance type %s' % type(stream_instance))
python
def link(self, stream_instance): """Set my input stream""" if isinstance(stream_instance, collections.Iterable): self.input_stream = stream_instance elif getattr(stream_instance, 'output_stream', None): self.input_stream = stream_instance.output_stream else: raise RuntimeError('Calling link() with unknown instance type %s' % type(stream_instance))
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Set my input stream
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b0227847b0c43083b456f0bae52daee0b62a3e03
https://github.com/SuperCowPowers/chains/blob/b0227847b0c43083b456f0bae52daee0b62a3e03/chains/links/link.py#L18-L25
train
48,441
ajenhl/tacl
tacl/catalogue.py
Catalogue.generate
def generate(self, path, label): """Creates default data from the corpus at `path`, marking all works with `label`. :param path: path to a corpus directory :type path: `str` :param label: label to categorise each work as :type label: `str` """ for filename in os.listdir(path): self[filename] = label
python
def generate(self, path, label): """Creates default data from the corpus at `path`, marking all works with `label`. :param path: path to a corpus directory :type path: `str` :param label: label to categorise each work as :type label: `str` """ for filename in os.listdir(path): self[filename] = label
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Creates default data from the corpus at `path`, marking all works with `label`. :param path: path to a corpus directory :type path: `str` :param label: label to categorise each work as :type label: `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/catalogue.py#L15-L26
train
48,442
ajenhl/tacl
tacl/catalogue.py
Catalogue.get_works_by_label
def get_works_by_label(self, label): """Returns a list of works associated with `label`. :param label: label of works to be returned :type label: `str` :rtype: `list` of `str` """ return [work for work, c_label in self.items() if c_label == label]
python
def get_works_by_label(self, label): """Returns a list of works associated with `label`. :param label: label of works to be returned :type label: `str` :rtype: `list` of `str` """ return [work for work, c_label in self.items() if c_label == label]
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Returns a list of works associated with `label`. :param label: label of works to be returned :type label: `str` :rtype: `list` of `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/catalogue.py#L28-L36
train
48,443
ajenhl/tacl
tacl/catalogue.py
Catalogue.load
def load(self, path): """Loads the data from `path` into the catalogue. :param path: path to catalogue file :type path: `str` """ fieldnames = ['work', 'label'] with open(path, 'r', encoding='utf-8', newline='') as fh: reader = csv.DictReader(fh, delimiter=' ', fieldnames=fieldnames, skipinitialspace=True) for row in reader: work, label = row['work'], row['label'] if label: if label not in self._ordered_labels: self._ordered_labels.append(label) if work in self: raise MalformedCatalogueError( CATALOGUE_WORK_RELABELLED_ERROR.format(work)) self[work] = label
python
def load(self, path): """Loads the data from `path` into the catalogue. :param path: path to catalogue file :type path: `str` """ fieldnames = ['work', 'label'] with open(path, 'r', encoding='utf-8', newline='') as fh: reader = csv.DictReader(fh, delimiter=' ', fieldnames=fieldnames, skipinitialspace=True) for row in reader: work, label = row['work'], row['label'] if label: if label not in self._ordered_labels: self._ordered_labels.append(label) if work in self: raise MalformedCatalogueError( CATALOGUE_WORK_RELABELLED_ERROR.format(work)) self[work] = label
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Loads the data from `path` into the catalogue. :param path: path to catalogue file :type path: `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/catalogue.py#L60-L79
train
48,444
ajenhl/tacl
tacl/catalogue.py
Catalogue.relabel
def relabel(self, label_map): """Returns a copy of the catalogue with the labels remapped according to `label_map`. `label_map` is a dictionary mapping existing labels to new labels. Any existing label that is not given a mapping is deleted from the resulting catalogue. :param label_map: mapping of labels to new labels :type label_map: `dict` :rtype: `tacl.Catalogue` """ catalogue = copy.deepcopy(self) to_delete = set() for work, old_label in catalogue.items(): if old_label in label_map: catalogue[work] = label_map[old_label] else: to_delete.add(catalogue[work]) for label in to_delete: catalogue.remove_label(label) return catalogue
python
def relabel(self, label_map): """Returns a copy of the catalogue with the labels remapped according to `label_map`. `label_map` is a dictionary mapping existing labels to new labels. Any existing label that is not given a mapping is deleted from the resulting catalogue. :param label_map: mapping of labels to new labels :type label_map: `dict` :rtype: `tacl.Catalogue` """ catalogue = copy.deepcopy(self) to_delete = set() for work, old_label in catalogue.items(): if old_label in label_map: catalogue[work] = label_map[old_label] else: to_delete.add(catalogue[work]) for label in to_delete: catalogue.remove_label(label) return catalogue
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Returns a copy of the catalogue with the labels remapped according to `label_map`. `label_map` is a dictionary mapping existing labels to new labels. Any existing label that is not given a mapping is deleted from the resulting catalogue. :param label_map: mapping of labels to new labels :type label_map: `dict` :rtype: `tacl.Catalogue`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/catalogue.py#L81-L103
train
48,445
ajenhl/tacl
tacl/catalogue.py
Catalogue.remove_label
def remove_label(self, label): """Removes `label` from the catalogue, by removing all works carrying it. :param label: label to remove :type label: `str` """ works_to_delete = [] for work, work_label in self.items(): if work_label == label: works_to_delete.append(work) for work in works_to_delete: del self[work] if self._ordered_labels: self._ordered_labels.remove(label)
python
def remove_label(self, label): """Removes `label` from the catalogue, by removing all works carrying it. :param label: label to remove :type label: `str` """ works_to_delete = [] for work, work_label in self.items(): if work_label == label: works_to_delete.append(work) for work in works_to_delete: del self[work] if self._ordered_labels: self._ordered_labels.remove(label)
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Removes `label` from the catalogue, by removing all works carrying it. :param label: label to remove :type label: `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/catalogue.py#L105-L120
train
48,446
ajenhl/tacl
tacl/catalogue.py
Catalogue.save
def save(self, path): """Saves this catalogue's data to `path`. :param path: file path to save catalogue data to :type path: `str` """ writer = csv.writer(open(path, 'w', newline=''), delimiter=' ') rows = list(self.items()) rows.sort(key=lambda x: x[0]) writer.writerows(rows)
python
def save(self, path): """Saves this catalogue's data to `path`. :param path: file path to save catalogue data to :type path: `str` """ writer = csv.writer(open(path, 'w', newline=''), delimiter=' ') rows = list(self.items()) rows.sort(key=lambda x: x[0]) writer.writerows(rows)
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Saves this catalogue's data to `path`. :param path: file path to save catalogue data to :type path: `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/catalogue.py#L122-L132
train
48,447
SuperCowPowers/chains
chains/links/dns_meta.py
DNSMeta._dns_weird
def _dns_weird(self, record): """Look for weird stuff in dns record using a set of criteria to mark the weird stuff""" weird = {} # Zero should always be 0 if record['flags']['zero'] != 0: weird['zero'] = record['flags']['zero'] # Trucated may indicate an exfil if record['flags']['truncated']: weird['trucnated'] = True # Weird Query Types weird_types = set(['DNS_NULL', 'DNS_HINFO', 'DNS_TXT', 'UNKNOWN']) for query in record['queries']: if query['type'] in weird_types: weird['query_type'] = query['type'] # Weird Query Classes weird_classes = set(['DNS_CHAOS', 'DNS_HESIOD', 'DNS_NONE', 'DNS_ANY']) for query in record['queries']: if query['class'] in weird_classes: weird['query_class'] = query['class'] # Weird Answer Types for section_name in ['answers', 'name_servers', 'additional']: for answer in record['answers'][section_name]: if answer['type'] in weird_types: weird['answer_type'] = answer['type'] # Weird Answer Classes for section_name in ['answers', 'name_servers', 'additional']: for answer in record['answers'][section_name]: if answer['class'] in weird_classes: weird['answer_class'] = answer['class'] # Is the subdomain name especially long or have high entropy? for query in record['queries']: subdomain = '.'.join(query['name'].split('.')[:-2]) length = len(subdomain) entropy = self.entropy(subdomain) if length > 35 and entropy > 3.5: weird['subdomain_length'] = length weird['subdomain'] = subdomain weird['subdomain_entropy'] = entropy weird['subdomain'] = subdomain # Return the weird stuff return weird
python
def _dns_weird(self, record): """Look for weird stuff in dns record using a set of criteria to mark the weird stuff""" weird = {} # Zero should always be 0 if record['flags']['zero'] != 0: weird['zero'] = record['flags']['zero'] # Trucated may indicate an exfil if record['flags']['truncated']: weird['trucnated'] = True # Weird Query Types weird_types = set(['DNS_NULL', 'DNS_HINFO', 'DNS_TXT', 'UNKNOWN']) for query in record['queries']: if query['type'] in weird_types: weird['query_type'] = query['type'] # Weird Query Classes weird_classes = set(['DNS_CHAOS', 'DNS_HESIOD', 'DNS_NONE', 'DNS_ANY']) for query in record['queries']: if query['class'] in weird_classes: weird['query_class'] = query['class'] # Weird Answer Types for section_name in ['answers', 'name_servers', 'additional']: for answer in record['answers'][section_name]: if answer['type'] in weird_types: weird['answer_type'] = answer['type'] # Weird Answer Classes for section_name in ['answers', 'name_servers', 'additional']: for answer in record['answers'][section_name]: if answer['class'] in weird_classes: weird['answer_class'] = answer['class'] # Is the subdomain name especially long or have high entropy? for query in record['queries']: subdomain = '.'.join(query['name'].split('.')[:-2]) length = len(subdomain) entropy = self.entropy(subdomain) if length > 35 and entropy > 3.5: weird['subdomain_length'] = length weird['subdomain'] = subdomain weird['subdomain_entropy'] = entropy weird['subdomain'] = subdomain # Return the weird stuff return weird
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Look for weird stuff in dns record using a set of criteria to mark the weird stuff
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b0227847b0c43083b456f0bae52daee0b62a3e03
https://github.com/SuperCowPowers/chains/blob/b0227847b0c43083b456f0bae52daee0b62a3e03/chains/links/dns_meta.py#L128-L176
train
48,448
ajenhl/tacl
tacl/corpus.py
Corpus.get_sigla
def get_sigla(self, work): """Returns a list of all of the sigla for `work`. :param work: name of work :type work: `str` :rtype: `list` of `str` """ return [os.path.splitext(os.path.basename(path))[0] for path in glob.glob(os.path.join(self._path, work, '*.txt'))]
python
def get_sigla(self, work): """Returns a list of all of the sigla for `work`. :param work: name of work :type work: `str` :rtype: `list` of `str` """ return [os.path.splitext(os.path.basename(path))[0] for path in glob.glob(os.path.join(self._path, work, '*.txt'))]
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Returns a list of all of the sigla for `work`. :param work: name of work :type work: `str` :rtype: `list` of `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/corpus.py#L24-L33
train
48,449
ajenhl/tacl
tacl/corpus.py
Corpus.get_witness
def get_witness(self, work, siglum, text_class=WitnessText): """Returns a `WitnessText` representing the file associated with `work` and `siglum`. Combined, `work` and `siglum` form the basis of a filename for retrieving the text. :param work: name of work :type work: `str` :param siglum: siglum of witness :type siglum: `str` :rtype: `WitnessText` """ filename = os.path.join(work, siglum + '.txt') self._logger.debug('Creating WitnessText object from {}'.format( filename)) with open(os.path.join(self._path, filename), encoding='utf-8') \ as fh: content = fh.read() return text_class(work, siglum, content, self._tokenizer)
python
def get_witness(self, work, siglum, text_class=WitnessText): """Returns a `WitnessText` representing the file associated with `work` and `siglum`. Combined, `work` and `siglum` form the basis of a filename for retrieving the text. :param work: name of work :type work: `str` :param siglum: siglum of witness :type siglum: `str` :rtype: `WitnessText` """ filename = os.path.join(work, siglum + '.txt') self._logger.debug('Creating WitnessText object from {}'.format( filename)) with open(os.path.join(self._path, filename), encoding='utf-8') \ as fh: content = fh.read() return text_class(work, siglum, content, self._tokenizer)
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Returns a `WitnessText` representing the file associated with `work` and `siglum`. Combined, `work` and `siglum` form the basis of a filename for retrieving the text. :param work: name of work :type work: `str` :param siglum: siglum of witness :type siglum: `str` :rtype: `WitnessText`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/corpus.py#L35-L55
train
48,450
ajenhl/tacl
tacl/corpus.py
Corpus.get_witnesses
def get_witnesses(self, name='*'): """Returns a generator supplying `WitnessText` objects for each work in the corpus. :rtype: `generator` of `WitnessText` """ for filepath in glob.glob(os.path.join(self._path, name, '*.txt')): if os.path.isfile(filepath): name = os.path.split(os.path.split(filepath)[0])[1] siglum = os.path.splitext(os.path.basename(filepath))[0] yield self.get_witness(name, siglum)
python
def get_witnesses(self, name='*'): """Returns a generator supplying `WitnessText` objects for each work in the corpus. :rtype: `generator` of `WitnessText` """ for filepath in glob.glob(os.path.join(self._path, name, '*.txt')): if os.path.isfile(filepath): name = os.path.split(os.path.split(filepath)[0])[1] siglum = os.path.splitext(os.path.basename(filepath))[0] yield self.get_witness(name, siglum)
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Returns a generator supplying `WitnessText` objects for each work in the corpus. :rtype: `generator` of `WitnessText`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/corpus.py#L57-L68
train
48,451
ajenhl/tacl
tacl/corpus.py
Corpus.get_works
def get_works(self): """Returns a list of the names of all works in the corpus. :rtype: `list` of `str` """ return [os.path.split(filepath)[1] for filepath in glob.glob(os.path.join(self._path, '*')) if os.path.isdir(filepath)]
python
def get_works(self): """Returns a list of the names of all works in the corpus. :rtype: `list` of `str` """ return [os.path.split(filepath)[1] for filepath in glob.glob(os.path.join(self._path, '*')) if os.path.isdir(filepath)]
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Returns a list of the names of all works in the corpus. :rtype: `list` of `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/corpus.py#L70-L78
train
48,452
ajenhl/tacl
tacl/decorators.py
requires_columns
def requires_columns(required_cols): """Decorator that raises a `MalformedResultsError` if any of `required_cols` is not present as a column in the matches of the `Results` object bearing the decorated method. :param required_cols: names of required columns :type required_cols: `list` of `str` """ def dec(f): @wraps(f) def decorated_function(*args, **kwargs): actual_cols = list(args[0]._matches.columns) missing_cols = [] for required_col in required_cols: if required_col not in actual_cols: missing_cols.append('"{}"'.format(required_col)) if missing_cols: raise MalformedResultsError( constants.MISSING_REQUIRED_COLUMNS_ERROR.format( ', '.join(missing_cols))) return f(*args, **kwargs) return decorated_function return dec
python
def requires_columns(required_cols): """Decorator that raises a `MalformedResultsError` if any of `required_cols` is not present as a column in the matches of the `Results` object bearing the decorated method. :param required_cols: names of required columns :type required_cols: `list` of `str` """ def dec(f): @wraps(f) def decorated_function(*args, **kwargs): actual_cols = list(args[0]._matches.columns) missing_cols = [] for required_col in required_cols: if required_col not in actual_cols: missing_cols.append('"{}"'.format(required_col)) if missing_cols: raise MalformedResultsError( constants.MISSING_REQUIRED_COLUMNS_ERROR.format( ', '.join(missing_cols))) return f(*args, **kwargs) return decorated_function return dec
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Decorator that raises a `MalformedResultsError` if any of `required_cols` is not present as a column in the matches of the `Results` object bearing the decorated method. :param required_cols: names of required columns :type required_cols: `list` of `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/decorators.py#L7-L30
train
48,453
SuperCowPowers/chains
chains/links/reverse_dns.py
ReverseDNS.process_for_rdns
def process_for_rdns(self): """Look through my input stream for the fields in ip_field_list and try to do a reverse dns lookup on those fields. """ # For each packet process the contents for item in self.input_stream: # Do for both the src and dst for endpoint in ['src', 'dst']: # Sanity check (might be an ARP, whatever... without a src/dst) if endpoint not in item['packet']: # Set the domain to None item['packet'][endpoint+self.domain_postfix] = None continue # Convert inet_address to str ip_address ip_address = net_utils.inet_to_str(item['packet'][endpoint]) # Is this already in our cache if self.ip_lookup_cache.get(ip_address): domain = self.ip_lookup_cache.get(ip_address) # Is the ip_address local or special elif net_utils.is_internal(ip_address): domain = 'internal' elif net_utils.is_special(ip_address): domain = net_utils.is_special(ip_address) # Look it up at this point else: domain = self._reverse_dns_lookup(ip_address) # Set the domain item['packet'][endpoint+self.domain_postfix] = domain # Cache it self.ip_lookup_cache.set(ip_address, domain) # All done yield item
python
def process_for_rdns(self): """Look through my input stream for the fields in ip_field_list and try to do a reverse dns lookup on those fields. """ # For each packet process the contents for item in self.input_stream: # Do for both the src and dst for endpoint in ['src', 'dst']: # Sanity check (might be an ARP, whatever... without a src/dst) if endpoint not in item['packet']: # Set the domain to None item['packet'][endpoint+self.domain_postfix] = None continue # Convert inet_address to str ip_address ip_address = net_utils.inet_to_str(item['packet'][endpoint]) # Is this already in our cache if self.ip_lookup_cache.get(ip_address): domain = self.ip_lookup_cache.get(ip_address) # Is the ip_address local or special elif net_utils.is_internal(ip_address): domain = 'internal' elif net_utils.is_special(ip_address): domain = net_utils.is_special(ip_address) # Look it up at this point else: domain = self._reverse_dns_lookup(ip_address) # Set the domain item['packet'][endpoint+self.domain_postfix] = domain # Cache it self.ip_lookup_cache.set(ip_address, domain) # All done yield item
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Look through my input stream for the fields in ip_field_list and try to do a reverse dns lookup on those fields.
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b0227847b0c43083b456f0bae52daee0b62a3e03
https://github.com/SuperCowPowers/chains/blob/b0227847b0c43083b456f0bae52daee0b62a3e03/chains/links/reverse_dns.py#L26-L68
train
48,454
ajenhl/tacl
tacl/colour.py
generate_colours
def generate_colours(n): """Return a list of `n` distinct colours, each represented as an RGB string suitable for use in CSS. Based on the code at http://martin.ankerl.com/2009/12/09/how-to-create-random-colors-programmatically/ :param n: number of colours to generate :type n: `int` :rtype: `list` of `str` """ colours = [] golden_ratio_conjugate = 0.618033988749895 h = 0.8 # Initial hue s = 0.7 # Fixed saturation v = 0.95 # Fixed value for i in range(n): h += golden_ratio_conjugate h %= 1 colours.append(hsv_to_rgb(h, s, v)) return colours
python
def generate_colours(n): """Return a list of `n` distinct colours, each represented as an RGB string suitable for use in CSS. Based on the code at http://martin.ankerl.com/2009/12/09/how-to-create-random-colors-programmatically/ :param n: number of colours to generate :type n: `int` :rtype: `list` of `str` """ colours = [] golden_ratio_conjugate = 0.618033988749895 h = 0.8 # Initial hue s = 0.7 # Fixed saturation v = 0.95 # Fixed value for i in range(n): h += golden_ratio_conjugate h %= 1 colours.append(hsv_to_rgb(h, s, v)) return colours
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/colour.py#L40-L61
train
48,455
SuperCowPowers/chains
chains/links/packet_tags.py
PacketTags.tag_stuff
def tag_stuff(self): """Look through my input stream for the fields to be tagged""" # For each packet in the pcap process the contents for item in self.input_stream: # Make sure it has a tags field (which is a set) if 'tags' not in item: item['tags'] = set() # For each tag_methods run it on the item for tag_method in self.tag_methods: item['tags'].add(tag_method(item)) # Not interested in None tags if None in item['tags']: item['tags'].remove(None) # All done yield item
python
def tag_stuff(self): """Look through my input stream for the fields to be tagged""" # For each packet in the pcap process the contents for item in self.input_stream: # Make sure it has a tags field (which is a set) if 'tags' not in item: item['tags'] = set() # For each tag_methods run it on the item for tag_method in self.tag_methods: item['tags'].add(tag_method(item)) # Not interested in None tags if None in item['tags']: item['tags'].remove(None) # All done yield item
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Look through my input stream for the fields to be tagged
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b0227847b0c43083b456f0bae52daee0b62a3e03
https://github.com/SuperCowPowers/chains/blob/b0227847b0c43083b456f0bae52daee0b62a3e03/chains/links/packet_tags.py#L29-L47
train
48,456
SuperCowPowers/chains
chains/links/packet_tags.py
PacketTags._tag_net_direction
def _tag_net_direction(data): """Create a tag based on the direction of the traffic""" # IP or IPv6 src = data['packet']['src_domain'] dst = data['packet']['dst_domain'] if src == 'internal': if dst == 'internal' or 'multicast' in dst or 'broadcast' in dst: return 'internal' else: return 'outgoing' elif dst == 'internal': return 'incoming' else: return None
python
def _tag_net_direction(data): """Create a tag based on the direction of the traffic""" # IP or IPv6 src = data['packet']['src_domain'] dst = data['packet']['dst_domain'] if src == 'internal': if dst == 'internal' or 'multicast' in dst or 'broadcast' in dst: return 'internal' else: return 'outgoing' elif dst == 'internal': return 'incoming' else: return None
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Create a tag based on the direction of the traffic
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b0227847b0c43083b456f0bae52daee0b62a3e03
https://github.com/SuperCowPowers/chains/blob/b0227847b0c43083b456f0bae52daee0b62a3e03/chains/links/packet_tags.py#L50-L64
train
48,457
ajenhl/tacl
tacl/tei_corpus.py
TEICorpus._output_work
def _output_work(self, work, root): """Saves the TEI XML document `root` at the path `work`.""" output_filename = os.path.join(self._output_dir, work) tree = etree.ElementTree(root) tree.write(output_filename, encoding='utf-8', pretty_print=True)
python
def _output_work(self, work, root): """Saves the TEI XML document `root` at the path `work`.""" output_filename = os.path.join(self._output_dir, work) tree = etree.ElementTree(root) tree.write(output_filename, encoding='utf-8', pretty_print=True)
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Saves the TEI XML document `root` at the path `work`.
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/tei_corpus.py#L141-L145
train
48,458
ajenhl/tacl
tacl/tei_corpus.py
TEICorpus._populate_header
def _populate_header(self, root): """Populate the teiHeader of the teiCorpus with useful information from the teiHeader of the first TEI part.""" # If this gets more complicated, it should be handled via an XSLT. title_stmt = root.xpath( 'tei:teiHeader/tei:fileDesc/tei:titleStmt', namespaces=constants.NAMESPACES)[0] # There is no guarantee that a title or author is specified, # in which case do nothing. try: title_stmt[0].text = root.xpath( 'tei:TEI[1]/tei:teiHeader/tei:fileDesc/tei:titleStmt/' 'tei:title', namespaces=constants.NAMESPACES)[0].text except IndexError: pass try: title_stmt[1].text = root.xpath( 'tei:TEI[1]/tei:teiHeader/tei:fileDesc/tei:titleStmt/' 'tei:author', namespaces=constants.NAMESPACES)[0].text except IndexError: pass return root
python
def _populate_header(self, root): """Populate the teiHeader of the teiCorpus with useful information from the teiHeader of the first TEI part.""" # If this gets more complicated, it should be handled via an XSLT. title_stmt = root.xpath( 'tei:teiHeader/tei:fileDesc/tei:titleStmt', namespaces=constants.NAMESPACES)[0] # There is no guarantee that a title or author is specified, # in which case do nothing. try: title_stmt[0].text = root.xpath( 'tei:TEI[1]/tei:teiHeader/tei:fileDesc/tei:titleStmt/' 'tei:title', namespaces=constants.NAMESPACES)[0].text except IndexError: pass try: title_stmt[1].text = root.xpath( 'tei:TEI[1]/tei:teiHeader/tei:fileDesc/tei:titleStmt/' 'tei:author', namespaces=constants.NAMESPACES)[0].text except IndexError: pass return root
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Populate the teiHeader of the teiCorpus with useful information from the teiHeader of the first TEI part.
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/tei_corpus.py#L147-L168
train
48,459
ajenhl/tacl
tacl/tei_corpus.py
TEICorpusCBETAGitHub._extract_work
def _extract_work(self, filename): """Returns the name of the work in `filename`. Some works are divided into multiple parts that need to be joined together. :param filename: filename of TEI :type filename: `str` :rtype: `tuple` of `str` """ basename = os.path.splitext(os.path.basename(filename))[0] match = self.work_pattern.search(basename) if match is None: self._logger.warning('Found an anomalous filename "{}"'.format( filename)) return None, None work = '{}{}'.format(match.group('prefix'), match.group('work')) return work, match.group('part')
python
def _extract_work(self, filename): """Returns the name of the work in `filename`. Some works are divided into multiple parts that need to be joined together. :param filename: filename of TEI :type filename: `str` :rtype: `tuple` of `str` """ basename = os.path.splitext(os.path.basename(filename))[0] match = self.work_pattern.search(basename) if match is None: self._logger.warning('Found an anomalous filename "{}"'.format( filename)) return None, None work = '{}{}'.format(match.group('prefix'), match.group('work')) return work, match.group('part')
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Returns the name of the work in `filename`. Some works are divided into multiple parts that need to be joined together. :param filename: filename of TEI :type filename: `str` :rtype: `tuple` of `str`
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/tei_corpus.py#L220-L238
train
48,460
ajenhl/tacl
tacl/tei_corpus.py
TEICorpusCBETAGitHub._handle_resps
def _handle_resps(self, root): """Returns `root` with a resp list added to the TEI header and @resp values changed to references.""" resps, bearers = self.get_resps(root) if not resps: return root file_desc = root.xpath( '/tei:teiCorpus/tei:teiHeader/tei:fileDesc', namespaces=constants.NAMESPACES)[0] edition_stmt = etree.Element(TEI + 'editionStmt') file_desc.insert(1, edition_stmt) for index, (resp_resp, resp_name) in enumerate(resps): resp_stmt = etree.SubElement(edition_stmt, TEI + 'respStmt') xml_id = 'resp{}'.format(index+1) resp_stmt.set(constants.XML + 'id', xml_id) resp = etree.SubElement(resp_stmt, TEI + 'resp') resp.text = resp_resp name = etree.SubElement(resp_stmt, TEI + 'name') name.text = resp_name resp_data = '{{{}|{}}}'.format(resp_resp, resp_name) self._update_refs(root, bearers, 'resp', resp_data, xml_id) return root
python
def _handle_resps(self, root): """Returns `root` with a resp list added to the TEI header and @resp values changed to references.""" resps, bearers = self.get_resps(root) if not resps: return root file_desc = root.xpath( '/tei:teiCorpus/tei:teiHeader/tei:fileDesc', namespaces=constants.NAMESPACES)[0] edition_stmt = etree.Element(TEI + 'editionStmt') file_desc.insert(1, edition_stmt) for index, (resp_resp, resp_name) in enumerate(resps): resp_stmt = etree.SubElement(edition_stmt, TEI + 'respStmt') xml_id = 'resp{}'.format(index+1) resp_stmt.set(constants.XML + 'id', xml_id) resp = etree.SubElement(resp_stmt, TEI + 'resp') resp.text = resp_resp name = etree.SubElement(resp_stmt, TEI + 'name') name.text = resp_name resp_data = '{{{}|{}}}'.format(resp_resp, resp_name) self._update_refs(root, bearers, 'resp', resp_data, xml_id) return root
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Returns `root` with a resp list added to the TEI header and @resp values changed to references.
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/tei_corpus.py#L258-L279
train
48,461
ajenhl/tacl
tacl/tei_corpus.py
TEICorpusCBETAGitHub._tidy
def _tidy(self, work, file_path): """Transforms the file at `file_path` into simpler XML and returns that. """ output_file = os.path.join(self._output_dir, work) self._logger.info('Tidying file {} into {}'.format( file_path, output_file)) try: tei_doc = etree.parse(file_path) except etree.XMLSyntaxError as err: self._logger.error('XML file "{}" is invalid: {}'.format( file_path, err)) raise return self.transform(tei_doc).getroot()
python
def _tidy(self, work, file_path): """Transforms the file at `file_path` into simpler XML and returns that. """ output_file = os.path.join(self._output_dir, work) self._logger.info('Tidying file {} into {}'.format( file_path, output_file)) try: tei_doc = etree.parse(file_path) except etree.XMLSyntaxError as err: self._logger.error('XML file "{}" is invalid: {}'.format( file_path, err)) raise return self.transform(tei_doc).getroot()
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Transforms the file at `file_path` into simpler XML and returns that.
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b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2
https://github.com/ajenhl/tacl/blob/b8a343248e77f1c07a5a4ac133a9ad6e0b4781c2/tacl/tei_corpus.py#L281-L295
train
48,462
SuperCowPowers/chains
chains/utils/flow_utils.py
Flow.add_packet
def add_packet(self, packet): """Add a packet to this flow""" # First packet? if not self.meta['flow_id']: self.meta['flow_id'] = flow_tuple(packet) self.meta['src'] = self.meta['flow_id'][0] self.meta['dst'] = self.meta['flow_id'][1] self.meta['src_domain'] = packet['packet']['src_domain'] self.meta['dst_domain'] = packet['packet']['dst_domain'] self.meta['sport'] = self.meta['flow_id'][2] self.meta['dport'] = self.meta['flow_id'][3] self.meta['protocol'] = self.meta['flow_id'][4] self.meta['direction'] = self._cts_or_stc(packet) self.meta['start'] = packet['timestamp'] self.meta['end'] = packet['timestamp'] # Add the packet self.meta['packet_list'].append(packet) if packet['timestamp'] < self.meta['start']: self.meta['start'] = packet['timestamp'] if packet['timestamp'] > self.meta['end']: self.meta['end'] = packet['timestamp'] # State of connection/flow if self.meta['protocol'] == 'TCP': flags = packet['transport']['flags'] if 'syn' in flags: self.meta['state'] = 'partial_syn' self.meta['direction'] = 'CTS' elif 'fin' in flags: # print('--- FIN RECEIVED %s ---' % str(self.meta['flow_id)) self.meta['state'] = 'complete' if self.meta['state'] == 'partial_syn' else 'partial' self.meta['timeout'] = datetime.now() + timedelta(seconds=1) elif 'syn_ack' in flags: self.meta['state'] = 'partial_syn' self.meta['direction'] = 'STC' elif 'fin_ack'in flags: # print('--- FIN_ACK RECEIVED %s ---' % str(self.meta['flow_id)) self.meta['state'] = 'complete' if self.meta['state'] == 'partial_syn' else 'partial' self.meta['timeout'] = datetime.now() + timedelta(seconds=1) elif 'rst' in flags: # print('--- RESET RECEIVED %s ---' % str(self.meta['flow_id)) self.meta['state'] = 'partial' self.meta['timeout'] = datetime.now() + timedelta(seconds=1) # Only collect UDP and TCP if self.meta['protocol'] not in ['UDP', 'TCP']: self.meta['timeout'] = datetime.now()
python
def add_packet(self, packet): """Add a packet to this flow""" # First packet? if not self.meta['flow_id']: self.meta['flow_id'] = flow_tuple(packet) self.meta['src'] = self.meta['flow_id'][0] self.meta['dst'] = self.meta['flow_id'][1] self.meta['src_domain'] = packet['packet']['src_domain'] self.meta['dst_domain'] = packet['packet']['dst_domain'] self.meta['sport'] = self.meta['flow_id'][2] self.meta['dport'] = self.meta['flow_id'][3] self.meta['protocol'] = self.meta['flow_id'][4] self.meta['direction'] = self._cts_or_stc(packet) self.meta['start'] = packet['timestamp'] self.meta['end'] = packet['timestamp'] # Add the packet self.meta['packet_list'].append(packet) if packet['timestamp'] < self.meta['start']: self.meta['start'] = packet['timestamp'] if packet['timestamp'] > self.meta['end']: self.meta['end'] = packet['timestamp'] # State of connection/flow if self.meta['protocol'] == 'TCP': flags = packet['transport']['flags'] if 'syn' in flags: self.meta['state'] = 'partial_syn' self.meta['direction'] = 'CTS' elif 'fin' in flags: # print('--- FIN RECEIVED %s ---' % str(self.meta['flow_id)) self.meta['state'] = 'complete' if self.meta['state'] == 'partial_syn' else 'partial' self.meta['timeout'] = datetime.now() + timedelta(seconds=1) elif 'syn_ack' in flags: self.meta['state'] = 'partial_syn' self.meta['direction'] = 'STC' elif 'fin_ack'in flags: # print('--- FIN_ACK RECEIVED %s ---' % str(self.meta['flow_id)) self.meta['state'] = 'complete' if self.meta['state'] == 'partial_syn' else 'partial' self.meta['timeout'] = datetime.now() + timedelta(seconds=1) elif 'rst' in flags: # print('--- RESET RECEIVED %s ---' % str(self.meta['flow_id)) self.meta['state'] = 'partial' self.meta['timeout'] = datetime.now() + timedelta(seconds=1) # Only collect UDP and TCP if self.meta['protocol'] not in ['UDP', 'TCP']: self.meta['timeout'] = datetime.now()
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Add a packet to this flow
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b0227847b0c43083b456f0bae52daee0b62a3e03
https://github.com/SuperCowPowers/chains/blob/b0227847b0c43083b456f0bae52daee0b62a3e03/chains/utils/flow_utils.py#L48-L96
train
48,463
gristlabs/asttokens
asttokens/asttokens.py
ASTTokens._generate_tokens
def _generate_tokens(self, text): """ Generates tokens for the given code. """ # This is technically an undocumented API for Python3, but allows us to use the same API as for # Python2. See http://stackoverflow.com/a/4952291/328565. for index, tok in enumerate(tokenize.generate_tokens(io.StringIO(text).readline)): tok_type, tok_str, start, end, line = tok yield Token(tok_type, tok_str, start, end, line, index, self._line_numbers.line_to_offset(start[0], start[1]), self._line_numbers.line_to_offset(end[0], end[1]))
python
def _generate_tokens(self, text): """ Generates tokens for the given code. """ # This is technically an undocumented API for Python3, but allows us to use the same API as for # Python2. See http://stackoverflow.com/a/4952291/328565. for index, tok in enumerate(tokenize.generate_tokens(io.StringIO(text).readline)): tok_type, tok_str, start, end, line = tok yield Token(tok_type, tok_str, start, end, line, index, self._line_numbers.line_to_offset(start[0], start[1]), self._line_numbers.line_to_offset(end[0], end[1]))
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Generates tokens for the given code.
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c8697dcf799a63d432727abb1d972adb3e85970a
https://github.com/gristlabs/asttokens/blob/c8697dcf799a63d432727abb1d972adb3e85970a/asttokens/asttokens.py#L79-L89
train
48,464
gristlabs/asttokens
asttokens/asttokens.py
ASTTokens.next_token
def next_token(self, tok, include_extra=False): """ Returns the next token after the given one. If include_extra is True, includes non-coding tokens from the tokenize module, such as NL and COMMENT. """ i = tok.index + 1 if not include_extra: while is_non_coding_token(self._tokens[i].type): i += 1 return self._tokens[i]
python
def next_token(self, tok, include_extra=False): """ Returns the next token after the given one. If include_extra is True, includes non-coding tokens from the tokenize module, such as NL and COMMENT. """ i = tok.index + 1 if not include_extra: while is_non_coding_token(self._tokens[i].type): i += 1 return self._tokens[i]
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Returns the next token after the given one. If include_extra is True, includes non-coding tokens from the tokenize module, such as NL and COMMENT.
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c8697dcf799a63d432727abb1d972adb3e85970a
https://github.com/gristlabs/asttokens/blob/c8697dcf799a63d432727abb1d972adb3e85970a/asttokens/asttokens.py#L134-L143
train
48,465
gristlabs/asttokens
asttokens/asttokens.py
ASTTokens.token_range
def token_range(self, first_token, last_token, include_extra=False): """ Yields all tokens in order from first_token through and including last_token. If include_extra is True, includes non-coding tokens such as tokenize.NL and .COMMENT. """ for i in xrange(first_token.index, last_token.index + 1): if include_extra or not is_non_coding_token(self._tokens[i].type): yield self._tokens[i]
python
def token_range(self, first_token, last_token, include_extra=False): """ Yields all tokens in order from first_token through and including last_token. If include_extra is True, includes non-coding tokens such as tokenize.NL and .COMMENT. """ for i in xrange(first_token.index, last_token.index + 1): if include_extra or not is_non_coding_token(self._tokens[i].type): yield self._tokens[i]
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c8697dcf799a63d432727abb1d972adb3e85970a
https://github.com/gristlabs/asttokens/blob/c8697dcf799a63d432727abb1d972adb3e85970a/asttokens/asttokens.py#L168-L175
train
48,466
gristlabs/asttokens
asttokens/asttokens.py
ASTTokens.get_tokens
def get_tokens(self, node, include_extra=False): """ Yields all tokens making up the given node. If include_extra is True, includes non-coding tokens such as tokenize.NL and .COMMENT. """ return self.token_range(node.first_token, node.last_token, include_extra=include_extra)
python
def get_tokens(self, node, include_extra=False): """ Yields all tokens making up the given node. If include_extra is True, includes non-coding tokens such as tokenize.NL and .COMMENT. """ return self.token_range(node.first_token, node.last_token, include_extra=include_extra)
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Yields all tokens making up the given node. If include_extra is True, includes non-coding tokens such as tokenize.NL and .COMMENT.
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c8697dcf799a63d432727abb1d972adb3e85970a
https://github.com/gristlabs/asttokens/blob/c8697dcf799a63d432727abb1d972adb3e85970a/asttokens/asttokens.py#L177-L182
train
48,467
gristlabs/asttokens
asttokens/line_numbers.py
LineNumbers.from_utf8_col
def from_utf8_col(self, line, utf8_column): """ Given a 1-based line number and 0-based utf8 column, returns a 0-based unicode column. """ offsets = self._utf8_offset_cache.get(line) if offsets is None: end_offset = self._line_offsets[line] if line < len(self._line_offsets) else self._text_len line_text = self._text[self._line_offsets[line - 1] : end_offset] offsets = [i for i,c in enumerate(line_text) for byte in c.encode('utf8')] offsets.append(len(line_text)) self._utf8_offset_cache[line] = offsets return offsets[max(0, min(len(offsets)-1, utf8_column))]
python
def from_utf8_col(self, line, utf8_column): """ Given a 1-based line number and 0-based utf8 column, returns a 0-based unicode column. """ offsets = self._utf8_offset_cache.get(line) if offsets is None: end_offset = self._line_offsets[line] if line < len(self._line_offsets) else self._text_len line_text = self._text[self._line_offsets[line - 1] : end_offset] offsets = [i for i,c in enumerate(line_text) for byte in c.encode('utf8')] offsets.append(len(line_text)) self._utf8_offset_cache[line] = offsets return offsets[max(0, min(len(offsets)-1, utf8_column))]
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Given a 1-based line number and 0-based utf8 column, returns a 0-based unicode column.
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c8697dcf799a63d432727abb1d972adb3e85970a
https://github.com/gristlabs/asttokens/blob/c8697dcf799a63d432727abb1d972adb3e85970a/asttokens/line_numbers.py#L35-L48
train
48,468
gristlabs/asttokens
asttokens/line_numbers.py
LineNumbers.line_to_offset
def line_to_offset(self, line, column): """ Converts 1-based line number and 0-based column to 0-based character offset into text. """ line -= 1 if line >= len(self._line_offsets): return self._text_len elif line < 0: return 0 else: return min(self._line_offsets[line] + max(0, column), self._text_len)
python
def line_to_offset(self, line, column): """ Converts 1-based line number and 0-based column to 0-based character offset into text. """ line -= 1 if line >= len(self._line_offsets): return self._text_len elif line < 0: return 0 else: return min(self._line_offsets[line] + max(0, column), self._text_len)
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Converts 1-based line number and 0-based column to 0-based character offset into text.
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c8697dcf799a63d432727abb1d972adb3e85970a
https://github.com/gristlabs/asttokens/blob/c8697dcf799a63d432727abb1d972adb3e85970a/asttokens/line_numbers.py#L50-L60
train
48,469
gristlabs/asttokens
asttokens/util.py
match_token
def match_token(token, tok_type, tok_str=None): """Returns true if token is of the given type and, if a string is given, has that string.""" return token.type == tok_type and (tok_str is None or token.string == tok_str)
python
def match_token(token, tok_type, tok_str=None): """Returns true if token is of the given type and, if a string is given, has that string.""" return token.type == tok_type and (tok_str is None or token.string == tok_str)
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Returns true if token is of the given type and, if a string is given, has that string.
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c8697dcf799a63d432727abb1d972adb3e85970a
https://github.com/gristlabs/asttokens/blob/c8697dcf799a63d432727abb1d972adb3e85970a/asttokens/util.py#L45-L47
train
48,470
gristlabs/asttokens
asttokens/util.py
expect_token
def expect_token(token, tok_type, tok_str=None): """ Verifies that the given token is of the expected type. If tok_str is given, the token string is verified too. If the token doesn't match, raises an informative ValueError. """ if not match_token(token, tok_type, tok_str): raise ValueError("Expected token %s, got %s on line %s col %s" % ( token_repr(tok_type, tok_str), str(token), token.start[0], token.start[1] + 1))
python
def expect_token(token, tok_type, tok_str=None): """ Verifies that the given token is of the expected type. If tok_str is given, the token string is verified too. If the token doesn't match, raises an informative ValueError. """ if not match_token(token, tok_type, tok_str): raise ValueError("Expected token %s, got %s on line %s col %s" % ( token_repr(tok_type, tok_str), str(token), token.start[0], token.start[1] + 1))
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Verifies that the given token is of the expected type. If tok_str is given, the token string is verified too. If the token doesn't match, raises an informative ValueError.
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c8697dcf799a63d432727abb1d972adb3e85970a
https://github.com/gristlabs/asttokens/blob/c8697dcf799a63d432727abb1d972adb3e85970a/asttokens/util.py#L50-L58
train
48,471
gristlabs/asttokens
asttokens/util.py
visit_tree
def visit_tree(node, previsit, postvisit): """ Scans the tree under the node depth-first using an explicit stack. It avoids implicit recursion via the function call stack to avoid hitting 'maximum recursion depth exceeded' error. It calls ``previsit()`` and ``postvisit()`` as follows: * ``previsit(node, par_value)`` - should return ``(par_value, value)`` ``par_value`` is as returned from ``previsit()`` of the parent. * ``postvisit(node, par_value, value)`` - should return ``value`` ``par_value`` is as returned from ``previsit()`` of the parent, and ``value`` is as returned from ``previsit()`` of this node itself. The return ``value`` is ignored except the one for the root node, which is returned from the overall ``visit_tree()`` call. For the initial node, ``par_value`` is None. Either ``previsit`` and ``postvisit`` may be None. """ if not previsit: previsit = lambda node, pvalue: (None, None) if not postvisit: postvisit = lambda node, pvalue, value: None iter_children = iter_children_func(node) done = set() ret = None stack = [(node, None, _PREVISIT)] while stack: current, par_value, value = stack.pop() if value is _PREVISIT: assert current not in done # protect againt infinite loop in case of a bad tree. done.add(current) pvalue, post_value = previsit(current, par_value) stack.append((current, par_value, post_value)) # Insert all children in reverse order (so that first child ends up on top of the stack). ins = len(stack) for n in iter_children(current): stack.insert(ins, (n, pvalue, _PREVISIT)) else: ret = postvisit(current, par_value, value) return ret
python
def visit_tree(node, previsit, postvisit): """ Scans the tree under the node depth-first using an explicit stack. It avoids implicit recursion via the function call stack to avoid hitting 'maximum recursion depth exceeded' error. It calls ``previsit()`` and ``postvisit()`` as follows: * ``previsit(node, par_value)`` - should return ``(par_value, value)`` ``par_value`` is as returned from ``previsit()`` of the parent. * ``postvisit(node, par_value, value)`` - should return ``value`` ``par_value`` is as returned from ``previsit()`` of the parent, and ``value`` is as returned from ``previsit()`` of this node itself. The return ``value`` is ignored except the one for the root node, which is returned from the overall ``visit_tree()`` call. For the initial node, ``par_value`` is None. Either ``previsit`` and ``postvisit`` may be None. """ if not previsit: previsit = lambda node, pvalue: (None, None) if not postvisit: postvisit = lambda node, pvalue, value: None iter_children = iter_children_func(node) done = set() ret = None stack = [(node, None, _PREVISIT)] while stack: current, par_value, value = stack.pop() if value is _PREVISIT: assert current not in done # protect againt infinite loop in case of a bad tree. done.add(current) pvalue, post_value = previsit(current, par_value) stack.append((current, par_value, post_value)) # Insert all children in reverse order (so that first child ends up on top of the stack). ins = len(stack) for n in iter_children(current): stack.insert(ins, (n, pvalue, _PREVISIT)) else: ret = postvisit(current, par_value, value) return ret
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c8697dcf799a63d432727abb1d972adb3e85970a
https://github.com/gristlabs/asttokens/blob/c8697dcf799a63d432727abb1d972adb3e85970a/asttokens/util.py#L144-L185
train
48,472
robin900/gspread-dataframe
gspread_dataframe.py
_cellrepr
def _cellrepr(value, allow_formulas): """ Get a string representation of dataframe value. :param :value: the value to represent :param :allow_formulas: if True, allow values starting with '=' to be interpreted as formulas; otherwise, escape them with an apostrophe to avoid formula interpretation. """ if pd.isnull(value) is True: return "" if isinstance(value, float): value = repr(value) else: value = str(value) if (not allow_formulas) and value.startswith('='): value = "'%s" % value return value
python
def _cellrepr(value, allow_formulas): """ Get a string representation of dataframe value. :param :value: the value to represent :param :allow_formulas: if True, allow values starting with '=' to be interpreted as formulas; otherwise, escape them with an apostrophe to avoid formula interpretation. """ if pd.isnull(value) is True: return "" if isinstance(value, float): value = repr(value) else: value = str(value) if (not allow_formulas) and value.startswith('='): value = "'%s" % value return value
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b64fef7ec196bfed69362aa35c593f448830a735
https://github.com/robin900/gspread-dataframe/blob/b64fef7ec196bfed69362aa35c593f448830a735/gspread_dataframe.py#L40-L57
train
48,473
robin900/gspread-dataframe
gspread_dataframe.py
_resize_to_minimum
def _resize_to_minimum(worksheet, rows=None, cols=None): """ Resize the worksheet to guarantee a minimum size, either in rows, or columns, or both. Both rows and cols are optional. """ # get the current size current_cols, current_rows = ( worksheet.col_count, worksheet.row_count ) if rows is not None and rows <= current_rows: rows = None if cols is not None and cols <= current_cols: cols = None if cols is not None or rows is not None: worksheet.resize(rows, cols)
python
def _resize_to_minimum(worksheet, rows=None, cols=None): """ Resize the worksheet to guarantee a minimum size, either in rows, or columns, or both. Both rows and cols are optional. """ # get the current size current_cols, current_rows = ( worksheet.col_count, worksheet.row_count ) if rows is not None and rows <= current_rows: rows = None if cols is not None and cols <= current_cols: cols = None if cols is not None or rows is not None: worksheet.resize(rows, cols)
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b64fef7ec196bfed69362aa35c593f448830a735
https://github.com/robin900/gspread-dataframe/blob/b64fef7ec196bfed69362aa35c593f448830a735/gspread_dataframe.py#L59-L77
train
48,474
robin900/gspread-dataframe
gspread_dataframe.py
get_as_dataframe
def get_as_dataframe(worksheet, evaluate_formulas=False, **options): """ Returns the worksheet contents as a DataFrame. :param worksheet: the worksheet. :param evaluate_formulas: if True, get the value of a cell after formula evaluation; otherwise get the formula itself if present. Defaults to False. :param \*\*options: all the options for pandas.io.parsers.TextParser, according to the version of pandas that is installed. (Note: TextParser supports only the default 'python' parser engine, not the C engine.) :returns: pandas.DataFrame """ all_values = _get_all_values(worksheet, evaluate_formulas) return TextParser(all_values, **options).read()
python
def get_as_dataframe(worksheet, evaluate_formulas=False, **options): """ Returns the worksheet contents as a DataFrame. :param worksheet: the worksheet. :param evaluate_formulas: if True, get the value of a cell after formula evaluation; otherwise get the formula itself if present. Defaults to False. :param \*\*options: all the options for pandas.io.parsers.TextParser, according to the version of pandas that is installed. (Note: TextParser supports only the default 'python' parser engine, not the C engine.) :returns: pandas.DataFrame """ all_values = _get_all_values(worksheet, evaluate_formulas) return TextParser(all_values, **options).read()
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b64fef7ec196bfed69362aa35c593f448830a735
https://github.com/robin900/gspread-dataframe/blob/b64fef7ec196bfed69362aa35c593f448830a735/gspread_dataframe.py#L118-L135
train
48,475
openregister/openregister-python
openregister/entry.py
Entry.timestamp
def timestamp(self, timestamp): """Entry timestamp as datetime.""" if timestamp is None: self._timestamp = datetime.utcnow() elif isinstance(timestamp, datetime): self._timestamp = timestamp else: self._timestamp = datetime.strptime(timestamp, fmt)
python
def timestamp(self, timestamp): """Entry timestamp as datetime.""" if timestamp is None: self._timestamp = datetime.utcnow() elif isinstance(timestamp, datetime): self._timestamp = timestamp else: self._timestamp = datetime.strptime(timestamp, fmt)
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/entry.py#L27-L34
train
48,476
openregister/openregister-python
openregister/entry.py
Entry.primitive
def primitive(self): """Entry as Python primitive.""" primitive = {} if self.entry_number is not None: primitive['entry-number'] = self.entry_number if self.item_hash is not None: primitive['item-hash'] = self.item_hash primitive['timestamp'] = self.timestamp.strftime(fmt) return primitive
python
def primitive(self): """Entry as Python primitive.""" primitive = {} if self.entry_number is not None: primitive['entry-number'] = self.entry_number if self.item_hash is not None: primitive['item-hash'] = self.item_hash primitive['timestamp'] = self.timestamp.strftime(fmt) return primitive
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/entry.py#L37-L47
train
48,477
openregister/openregister-python
openregister/entry.py
Entry.primitive
def primitive(self, primitive): """Entry from Python primitive.""" self.entry_number = primitive['entry-number'] self.item_hash = primitive['item-hash'] self.timestamp = primitive['timestamp']
python
def primitive(self, primitive): """Entry from Python primitive.""" self.entry_number = primitive['entry-number'] self.item_hash = primitive['item-hash'] self.timestamp = primitive['timestamp']
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/entry.py#L50-L54
train
48,478
openregister/openregister-python
openregister/client.py
Client.config
def config(self, name, suffix): "Return config variable value, defaulting to environment" var = '%s_%s' % (name, suffix) var = var.upper().replace('-', '_') if var in self._config: return self._config[var] return os.environ[var]
python
def config(self, name, suffix): "Return config variable value, defaulting to environment" var = '%s_%s' % (name, suffix) var = var.upper().replace('-', '_') if var in self._config: return self._config[var] return os.environ[var]
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/client.py#L16-L22
train
48,479
openregister/openregister-python
openregister/client.py
Client.index
def index(self, index, field, value): "Search for records matching a value in an index service" params = { "q": value, # search index has '_' instead of '-' in field names .. "q.options": "{fields:['%s']}" % (field.replace('-', '_')) } response = self.get(self.config(index, 'search_url'), params=params) results = [hit['fields'] for hit in response.json()['hits']['hit']] for result in results: for key in result: result[key.replace('_', '-')] = result.pop(key) return results
python
def index(self, index, field, value): "Search for records matching a value in an index service" params = { "q": value, # search index has '_' instead of '-' in field names .. "q.options": "{fields:['%s']}" % (field.replace('-', '_')) } response = self.get(self.config(index, 'search_url'), params=params) results = [hit['fields'] for hit in response.json()['hits']['hit']] for result in results: for key in result: result[key.replace('_', '-')] = result.pop(key) return results
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/client.py#L41-L56
train
48,480
openregister/openregister-python
openregister/item.py
Item.primitive
def primitive(self): """Python primitive representation.""" dict = {} for key, value in self.__dict__.items(): if not key.startswith('_'): dict[key] = copy(value) for key in dict: if isinstance(dict[key], (set)): dict[key] = sorted(list(dict[key])) return dict
python
def primitive(self): """Python primitive representation.""" dict = {} for key, value in self.__dict__.items(): if not key.startswith('_'): dict[key] = copy(value) for key in dict: if isinstance(dict[key], (set)): dict[key] = sorted(list(dict[key])) return dict
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/item.py#L49-L60
train
48,481
openregister/openregister-python
openregister/item.py
Item.primitive
def primitive(self, dictionary): """Item from Python primitive.""" self.__dict__ = {k: v for k, v in dictionary.items() if v}
python
def primitive(self, dictionary): """Item from Python primitive.""" self.__dict__ = {k: v for k, v in dictionary.items() if v}
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/item.py#L63-L65
train
48,482
openregister/openregister-python
openregister/record.py
Record.primitive
def primitive(self): """Record as Python primitive.""" primitive = copy(self.item.primitive) primitive.update(self.entry.primitive) return primitive
python
def primitive(self): """Record as Python primitive.""" primitive = copy(self.item.primitive) primitive.update(self.entry.primitive) return primitive
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Record as Python primitive.
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/record.py#L19-L23
train
48,483
openregister/openregister-python
openregister/record.py
Record.primitive
def primitive(self, primitive): """Record from Python primitive.""" self.entry = Entry() self.entry.primitive = primitive primitive = copy(primitive) for field in self.entry.fields: del primitive[field] self.item = Item() self.item.primitive = primitive
python
def primitive(self, primitive): """Record from Python primitive.""" self.entry = Entry() self.entry.primitive = primitive primitive = copy(primitive) for field in self.entry.fields: del primitive[field] self.item = Item() self.item.primitive = primitive
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Record from Python primitive.
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/record.py#L26-L36
train
48,484
openregister/openregister-python
openregister/representations/tsv.py
load
def load(self, text, fieldnames=None): """Item from TSV representation.""" lines = text.split('\n') fieldnames = load_line(lines[0]) values = load_line(lines[1]) self.__dict__ = dict(zip(fieldnames, values))
python
def load(self, text, fieldnames=None): """Item from TSV representation.""" lines = text.split('\n') fieldnames = load_line(lines[0]) values = load_line(lines[1]) self.__dict__ = dict(zip(fieldnames, values))
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/representations/tsv.py#L43-L48
train
48,485
openregister/openregister-python
openregister/representations/tsv.py
reader
def reader(stream, fieldnames=None): """Read Items from a stream containing TSV.""" if not fieldnames: fieldnames = load_line(stream.readline()) for line in stream: values = load_line(line) item = Item() item.__dict__ = dict(zip(fieldnames, values)) yield item
python
def reader(stream, fieldnames=None): """Read Items from a stream containing TSV.""" if not fieldnames: fieldnames = load_line(stream.readline()) for line in stream: values = load_line(line) item = Item() item.__dict__ = dict(zip(fieldnames, values)) yield item
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Read Items from a stream containing TSV.
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/representations/tsv.py#L51-L59
train
48,486
openregister/openregister-python
openregister/representations/tsv.py
dump
def dump(self): """TSV representation.""" dict = self.primitive if not dict: return '' return dump_line(self.keys) + dump_line(self.values)
python
def dump(self): """TSV representation.""" dict = self.primitive if not dict: return '' return dump_line(self.keys) + dump_line(self.values)
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TSV representation.
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/representations/tsv.py#L66-L71
train
48,487
openregister/openregister-python
openregister/representations/csv.py
load
def load(self, text, lineterminator='\r\n', quotechar='"', delimiter=",", escapechar=escapechar, quoting=csv.QUOTE_MINIMAL): """Item from CSV representation.""" f = io.StringIO(text) if not quotechar: quoting = csv.QUOTE_NONE reader = csv.DictReader( f, delimiter=delimiter, quotechar=quotechar, quoting=quoting, lineterminator=lineterminator) if reader.fieldnames: reader.fieldnames = [field.strip() for field in reader.fieldnames] try: self.primitive = next(reader) except StopIteration: self.primitive = {}
python
def load(self, text, lineterminator='\r\n', quotechar='"', delimiter=",", escapechar=escapechar, quoting=csv.QUOTE_MINIMAL): """Item from CSV representation.""" f = io.StringIO(text) if not quotechar: quoting = csv.QUOTE_NONE reader = csv.DictReader( f, delimiter=delimiter, quotechar=quotechar, quoting=quoting, lineterminator=lineterminator) if reader.fieldnames: reader.fieldnames = [field.strip() for field in reader.fieldnames] try: self.primitive = next(reader) except StopIteration: self.primitive = {}
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/representations/csv.py#L14-L40
train
48,488
openregister/openregister-python
openregister/representations/csv.py
dump
def dump(self, **kwargs): """CSV representation of a item.""" f = io.StringIO() w = Writer(f, self.keys, **kwargs) w.write(self) text = f.getvalue().lstrip() f.close() return text
python
def dump(self, **kwargs): """CSV representation of a item.""" f = io.StringIO() w = Writer(f, self.keys, **kwargs) w.write(self) text = f.getvalue().lstrip() f.close() return text
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/representations/csv.py#L70-L79
train
48,489
openregister/openregister-python
openregister/datatypes/digest.py
git_hash
def git_hash(blob): """Return git-hash compatible SHA-1 hexdigits for a blob of data.""" head = str("blob " + str(len(blob)) + "\0").encode("utf-8") return sha1(head + blob).hexdigest()
python
def git_hash(blob): """Return git-hash compatible SHA-1 hexdigits for a blob of data.""" head = str("blob " + str(len(blob)) + "\0").encode("utf-8") return sha1(head + blob).hexdigest()
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Return git-hash compatible SHA-1 hexdigits for a blob of data.
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/datatypes/digest.py#L5-L8
train
48,490
openregister/openregister-python
openregister/representations/json.py
dump
def dump(self): """Item as a JSON representation.""" return json.dumps( self.primitive, sort_keys=True, ensure_ascii=False, separators=(',', ':'))
python
def dump(self): """Item as a JSON representation.""" return json.dumps( self.primitive, sort_keys=True, ensure_ascii=False, separators=(',', ':'))
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Item as a JSON representation.
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/representations/json.py#L17-L23
train
48,491
openregister/openregister-python
openregister/representations/json.py
reader
def reader(stream): """Read Items from a stream containing a JSON array.""" string = stream.read() decoder = json.JSONDecoder().raw_decode index = START.match(string, 0).end() while index < len(string): obj, end = decoder(string, index) item = Item() item.primitive = obj yield item index = END.match(string, end).end()
python
def reader(stream): """Read Items from a stream containing a JSON array.""" string = stream.read() decoder = json.JSONDecoder().raw_decode index = START.match(string, 0).end() while index < len(string): obj, end = decoder(string, index) item = Item() item.primitive = obj yield item index = END.match(string, end).end()
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/representations/json.py#L26-L37
train
48,492
openregister/openregister-python
openregister/representations/jsonl.py
reader
def reader(stream): """Read Items from a stream containing lines of JSON.""" for line in stream: item = Item() item.json = line yield item
python
def reader(stream): """Read Items from a stream containing lines of JSON.""" for line in stream: item = Item() item.json = line yield item
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cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4
https://github.com/openregister/openregister-python/blob/cdb3ed9b454ff42cffdff4f25f7dbf8c22c517e4/openregister/representations/jsonl.py#L8-L13
train
48,493
sdispater/cachy
cachy/tag_set.py
TagSet.tag_id
def tag_id(self, name): """ Get the unique tag identifier for a given tag. :param name: The tag :type name: str :rtype: str """ return self._store.get(self.tag_key(name)) or self.reset_tag(name)
python
def tag_id(self, name): """ Get the unique tag identifier for a given tag. :param name: The tag :type name: str :rtype: str """ return self._store.get(self.tag_key(name)) or self.reset_tag(name)
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ee4b044d6aafa80125730a00b1f679a7bd852b8a
https://github.com/sdispater/cachy/blob/ee4b044d6aafa80125730a00b1f679a7bd852b8a/cachy/tag_set.py#L25-L34
train
48,494
sdispater/cachy
cachy/tag_set.py
TagSet.reset_tag
def reset_tag(self, name): """ Reset the tag and return the new tag identifier. :param name: The tag :type name: str :rtype: str """ id_ = str(uuid.uuid4()).replace('-', '') self._store.forever(self.tag_key(name), id_) return id_
python
def reset_tag(self, name): """ Reset the tag and return the new tag identifier. :param name: The tag :type name: str :rtype: str """ id_ = str(uuid.uuid4()).replace('-', '') self._store.forever(self.tag_key(name), id_) return id_
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Reset the tag and return the new tag identifier. :param name: The tag :type name: str :rtype: str
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ee4b044d6aafa80125730a00b1f679a7bd852b8a
https://github.com/sdispater/cachy/blob/ee4b044d6aafa80125730a00b1f679a7bd852b8a/cachy/tag_set.py#L52-L65
train
48,495
inveniosoftware/invenio-logging
invenio_logging/fs.py
InvenioLoggingFS.init_config
def init_config(self, app): """Initialize config.""" app.config.setdefault( 'LOGGING_FS_LEVEL', 'DEBUG' if app.debug else 'WARNING' ) for k in dir(config): if k.startswith('LOGGING_FS'): app.config.setdefault(k, getattr(config, k)) # Support injecting instance path and/or sys.prefix if app.config['LOGGING_FS_LOGFILE'] is not None: app.config['LOGGING_FS_LOGFILE'] = \ app.config['LOGGING_FS_LOGFILE'].format( instance_path=app.instance_path, sys_prefix=sys.prefix, )
python
def init_config(self, app): """Initialize config.""" app.config.setdefault( 'LOGGING_FS_LEVEL', 'DEBUG' if app.debug else 'WARNING' ) for k in dir(config): if k.startswith('LOGGING_FS'): app.config.setdefault(k, getattr(config, k)) # Support injecting instance path and/or sys.prefix if app.config['LOGGING_FS_LOGFILE'] is not None: app.config['LOGGING_FS_LOGFILE'] = \ app.config['LOGGING_FS_LOGFILE'].format( instance_path=app.instance_path, sys_prefix=sys.prefix, )
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59ee171ad4f9809f62a822964b5c68e5be672dd8
https://github.com/inveniosoftware/invenio-logging/blob/59ee171ad4f9809f62a822964b5c68e5be672dd8/invenio_logging/fs.py#L38-L54
train
48,496
inveniosoftware/invenio-logging
invenio_logging/fs.py
InvenioLoggingFS.install_handler
def install_handler(self, app): """Install log handler on Flask application.""" # Check if directory exists. basedir = dirname(app.config['LOGGING_FS_LOGFILE']) if not exists(basedir): raise ValueError( 'Log directory {0} does not exists.'.format(basedir)) handler = RotatingFileHandler( app.config['LOGGING_FS_LOGFILE'], backupCount=app.config['LOGGING_FS_BACKUPCOUNT'], maxBytes=app.config['LOGGING_FS_MAXBYTES'], delay=True, ) handler.setFormatter(logging.Formatter( '%(asctime)s %(levelname)s: %(message)s ' '[in %(pathname)s:%(lineno)d]' )) handler.setLevel(app.config['LOGGING_FS_LEVEL']) # Add handler to application logger app.logger.addHandler(handler) if app.config['LOGGING_FS_PYWARNINGS']: self.capture_pywarnings(handler) # Add request_id to log record app.logger.addFilter(add_request_id_filter)
python
def install_handler(self, app): """Install log handler on Flask application.""" # Check if directory exists. basedir = dirname(app.config['LOGGING_FS_LOGFILE']) if not exists(basedir): raise ValueError( 'Log directory {0} does not exists.'.format(basedir)) handler = RotatingFileHandler( app.config['LOGGING_FS_LOGFILE'], backupCount=app.config['LOGGING_FS_BACKUPCOUNT'], maxBytes=app.config['LOGGING_FS_MAXBYTES'], delay=True, ) handler.setFormatter(logging.Formatter( '%(asctime)s %(levelname)s: %(message)s ' '[in %(pathname)s:%(lineno)d]' )) handler.setLevel(app.config['LOGGING_FS_LEVEL']) # Add handler to application logger app.logger.addHandler(handler) if app.config['LOGGING_FS_PYWARNINGS']: self.capture_pywarnings(handler) # Add request_id to log record app.logger.addFilter(add_request_id_filter)
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59ee171ad4f9809f62a822964b5c68e5be672dd8
https://github.com/inveniosoftware/invenio-logging/blob/59ee171ad4f9809f62a822964b5c68e5be672dd8/invenio_logging/fs.py#L56-L83
train
48,497
sdispater/cachy
cachy/tagged_cache.py
TaggedCache.remember
def remember(self, key, minutes, callback): """ Get an item from the cache, or store the default value. :param key: The cache key :type key: str :param minutes: The lifetime in minutes of the cached value :type minutes: int or datetime :param callback: The default function :type callback: mixed :rtype: mixed """ # If the item exists in the cache we will just return this immediately # otherwise we will execute the given callback and cache the result # of that execution for the given number of minutes in storage. val = self.get(key) if val is not None: return val val = value(callback) self.put(key, val, minutes) return val
python
def remember(self, key, minutes, callback): """ Get an item from the cache, or store the default value. :param key: The cache key :type key: str :param minutes: The lifetime in minutes of the cached value :type minutes: int or datetime :param callback: The default function :type callback: mixed :rtype: mixed """ # If the item exists in the cache we will just return this immediately # otherwise we will execute the given callback and cache the result # of that execution for the given number of minutes in storage. val = self.get(key) if val is not None: return val val = value(callback) self.put(key, val, minutes) return val
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ee4b044d6aafa80125730a00b1f679a7bd852b8a
https://github.com/sdispater/cachy/blob/ee4b044d6aafa80125730a00b1f679a7bd852b8a/cachy/tagged_cache.py#L153-L179
train
48,498
sdispater/cachy
cachy/tagged_cache.py
TaggedCache.remember_forever
def remember_forever(self, key, callback): """ Get an item from the cache, or store the default value forever. :param key: The cache key :type key: str :param callback: The default function :type callback: mixed :rtype: mixed """ # If the item exists in the cache we will just return this immediately # otherwise we will execute the given callback and cache the result # of that execution forever. val = self.get(key) if val is not None: return val val = value(callback) self.forever(key, val) return val
python
def remember_forever(self, key, callback): """ Get an item from the cache, or store the default value forever. :param key: The cache key :type key: str :param callback: The default function :type callback: mixed :rtype: mixed """ # If the item exists in the cache we will just return this immediately # otherwise we will execute the given callback and cache the result # of that execution forever. val = self.get(key) if val is not None: return val val = value(callback) self.forever(key, val) return val
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ee4b044d6aafa80125730a00b1f679a7bd852b8a
https://github.com/sdispater/cachy/blob/ee4b044d6aafa80125730a00b1f679a7bd852b8a/cachy/tagged_cache.py#L181-L204
train
48,499