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mcs07/ChemDataExtractor | chemdataextractor/nlp/tag.py | ApTagger.save | def save(self, f):
"""Save pickled model to file."""
return pickle.dump((self.perceptron.weights, self.tagdict, self.classes, self.clusters), f, protocol=pickle.HIGHEST_PROTOCOL) | python | def save(self, f):
"""Save pickled model to file."""
return pickle.dump((self.perceptron.weights, self.tagdict, self.classes, self.clusters), f, protocol=pickle.HIGHEST_PROTOCOL) | [
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mcs07/ChemDataExtractor | chemdataextractor/nlp/tag.py | ApTagger.load | def load(self, model):
"""Load pickled model."""
self.perceptron.weights, self.tagdict, self.classes, self.clusters = load_model(model)
self.perceptron.classes = self.classes | python | def load(self, model):
"""Load pickled model."""
self.perceptron.weights, self.tagdict, self.classes, self.clusters = load_model(model)
self.perceptron.classes = self.classes | [
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mcs07/ChemDataExtractor | chemdataextractor/nlp/tag.py | CrfTagger.train | def train(self, sentences, model):
"""Train the CRF tagger using CRFSuite.
:params sentences: Annotated sentences.
:params model: Path to save pickled model.
"""
trainer = pycrfsuite.Trainer(verbose=True)
trainer.set_params(self.params)
for sentence in sentences:... | python | def train(self, sentences, model):
"""Train the CRF tagger using CRFSuite.
:params sentences: Annotated sentences.
:params model: Path to save pickled model.
"""
trainer = pycrfsuite.Trainer(verbose=True)
trainer.set_params(self.params)
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mcs07/ChemDataExtractor | chemdataextractor/nlp/tag.py | DictionaryTagger.load | def load(self, model):
"""Load pickled DAWG from disk."""
self._dawg.load(find_data(model))
self._loaded_model = True | python | def load(self, model):
"""Load pickled DAWG from disk."""
self._dawg.load(find_data(model))
self._loaded_model = True | [
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mcs07/ChemDataExtractor | chemdataextractor/nlp/tag.py | DictionaryTagger.build | def build(self, words):
"""Construct dictionary DAWG from tokenized words."""
words = [self._normalize(tokens) for tokens in words]
self._dawg = dawg.CompletionDAWG(words)
self._loaded_model = True | python | def build(self, words):
"""Construct dictionary DAWG from tokenized words."""
words = [self._normalize(tokens) for tokens in words]
self._dawg = dawg.CompletionDAWG(words)
self._loaded_model = True | [
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mcs07/ChemDataExtractor | chemdataextractor/nlp/tag.py | DictionaryTagger._normalize | def _normalize(self, tokens):
"""Normalization transform to apply to both dictionary words and input tokens."""
if self.case_sensitive:
return ' '.join(self.lexicon[t].normalized for t in tokens)
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return ' '.join(self.lexicon[t].lower for t in tokens) | python | def _normalize(self, tokens):
"""Normalization transform to apply to both dictionary words and input tokens."""
if self.case_sensitive:
return ' '.join(self.lexicon[t].normalized for t in tokens)
else:
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mcs07/ChemDataExtractor | chemdataextractor/parse/cem.py | standardize_role | def standardize_role(role):
"""Convert role text into standardized form."""
role = role.lower()
if any(c in role for c in {'synthesis', 'give', 'yield', 'afford', 'product', 'preparation of'}):
return 'product'
return role | python | def standardize_role(role):
"""Convert role text into standardized form."""
role = role.lower()
if any(c in role for c in {'synthesis', 'give', 'yield', 'afford', 'product', 'preparation of'}):
return 'product'
return role | [
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mcs07/ChemDataExtractor | chemdataextractor/cli/data.py | list | def list(ctx):
"""List active data packages."""
log.debug('chemdataextractor.data.list')
click.echo('Downloaded\tPackage')
for package in PACKAGES:
click.echo('%s\t%s' % (package.local_exists(), package.path)) | python | def list(ctx):
"""List active data packages."""
log.debug('chemdataextractor.data.list')
click.echo('Downloaded\tPackage')
for package in PACKAGES:
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mcs07/ChemDataExtractor | chemdataextractor/cli/data.py | download | def download(ctx):
"""Download data."""
log.debug('chemdataextractor.data.download')
count = 0
for package in PACKAGES:
success = package.download()
if success:
count += 1
click.echo('Successfully downloaded %s new data packages (%s existing)' % (count, len(PACKAGES) - co... | python | def download(ctx):
"""Download data."""
log.debug('chemdataextractor.data.download')
count = 0
for package in PACKAGES:
success = package.download()
if success:
count += 1
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mcs07/ChemDataExtractor | chemdataextractor/data.py | find_data | def find_data(path, warn=True):
"""Return the absolute path to a data file within the data directory."""
full_path = os.path.join(get_data_dir(), path)
if warn and not os.path.isfile(full_path):
for package in PACKAGES:
if path == package.path:
log.warn('%s doesn\'t exist... | python | def find_data(path, warn=True):
"""Return the absolute path to a data file within the data directory."""
full_path = os.path.join(get_data_dir(), path)
if warn and not os.path.isfile(full_path):
for package in PACKAGES:
if path == package.path:
log.warn('%s doesn\'t exist... | [
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mcs07/ChemDataExtractor | chemdataextractor/data.py | load_model | def load_model(path):
"""Load a model from a pickle file in the data directory. Cached so model is only loaded once."""
abspath = find_data(path)
cached = _model_cache.get(abspath)
if cached is not None:
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return cached
log.debug('Loading mod... | python | def load_model(path):
"""Load a model from a pickle file in the data directory. Cached so model is only loaded once."""
abspath = find_data(path)
cached = _model_cache.get(abspath)
if cached is not None:
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mcs07/ChemDataExtractor | chemdataextractor/text/normalize.py | ChemNormalizer.normalize | def normalize(self, text):
"""Normalize unicode, hyphens, whitespace, and some chemistry terms and formatting."""
text = super(ChemNormalizer, self).normalize(text)
# Normalize element spelling
if self.chem_spell:
text = re.sub(r'sulph', r'sulf', text, flags=re.I)
... | python | def normalize(self, text):
"""Normalize unicode, hyphens, whitespace, and some chemistry terms and formatting."""
text = super(ChemNormalizer, self).normalize(text)
# Normalize element spelling
if self.chem_spell:
text = re.sub(r'sulph', r'sulf', text, flags=re.I)
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mcs07/ChemDataExtractor | chemdataextractor/nlp/lexicon.py | Lexicon.add | def add(self, text):
"""Add text to the lexicon.
:param string text: The text to add.
"""
# logging.debug('Adding to lexicon: %s' % text)
if text not in self.lexemes:
normalized = self.normalized(text)
self.lexemes[text] = Lexeme(
text=tex... | python | def add(self, text):
"""Add text to the lexicon.
:param string text: The text to add.
"""
# logging.debug('Adding to lexicon: %s' % text)
if text not in self.lexemes:
normalized = self.normalized(text)
self.lexemes[text] = Lexeme(
text=tex... | [
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mcs07/ChemDataExtractor | chemdataextractor/doc/table.py | Table.serialize | def serialize(self):
"""Convert Table element to python dictionary."""
data = {
'type': self.__class__.__name__,
'caption': self.caption.serialize(),
'headings': [[cell.serialize() for cell in hrow] for hrow in self.headings],
'rows': [[cell.serialize() fo... | python | def serialize(self):
"""Convert Table element to python dictionary."""
data = {
'type': self.__class__.__name__,
'caption': self.caption.serialize(),
'headings': [[cell.serialize() for cell in hrow] for hrow in self.headings],
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mcs07/ChemDataExtractor | chemdataextractor/model.py | Compound.merge | def merge(self, other):
"""Merge data from another Compound into this Compound."""
log.debug('Merging: %s and %s' % (self.serialize(), other.serialize()))
for k in self.keys():
for new_item in other[k]:
if new_item not in self[k]:
self[k].append(ne... | python | def merge(self, other):
"""Merge data from another Compound into this Compound."""
log.debug('Merging: %s and %s' % (self.serialize(), other.serialize()))
for k in self.keys():
for new_item in other[k]:
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mcs07/ChemDataExtractor | chemdataextractor/model.py | Compound.merge_contextual | def merge_contextual(self, other):
"""Merge in contextual info from a template Compound."""
# TODO: This is currently dependent on our data model? Make more robust to schema changes
# Currently we assume all lists at Compound level, with 1 further potential nested level of lists
for k in... | python | def merge_contextual(self, other):
"""Merge in contextual info from a template Compound."""
# TODO: This is currently dependent on our data model? Make more robust to schema changes
# Currently we assume all lists at Compound level, with 1 further potential nested level of lists
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mcs07/ChemDataExtractor | chemdataextractor/model.py | Compound.is_id_only | def is_id_only(self):
"""Return True if identifier information only."""
for key, value in self.items():
if key not in {'names', 'labels', 'roles'} and value:
return False
if self.names or self.labels:
return True
return False | python | def is_id_only(self):
"""Return True if identifier information only."""
for key, value in self.items():
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return False
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mcs07/ChemDataExtractor | chemdataextractor/parse/actions.py | strip_stop | def strip_stop(tokens, start, result):
"""Remove trailing full stop from tokens."""
for e in result:
for child in e.iter():
if child.text.endswith('.'):
child.text = child.text[:-1]
return result | python | def strip_stop(tokens, start, result):
"""Remove trailing full stop from tokens."""
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mcs07/ChemDataExtractor | chemdataextractor/parse/actions.py | fix_whitespace | def fix_whitespace(tokens, start, result):
"""Fix whitespace around hyphens and commas. Can be used to remove whitespace tokenization artefacts."""
for e in result:
for child in e.iter():
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for hyphen in HYPHENS:
child.te... | python | def fix_whitespace(tokens, start, result):
"""Fix whitespace around hyphens and commas. Can be used to remove whitespace tokenization artefacts."""
for e in result:
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mcs07/ChemDataExtractor | chemdataextractor/reader/plaintext.py | PlainTextReader.detect | def detect(self, fstring, fname=None):
"""Have a stab at most files."""
if fname is not None and '.' in fname:
extension = fname.rsplit('.', 1)[1]
if extension in {'pdf', 'html', 'xml'}:
return False
return True | python | def detect(self, fstring, fname=None):
"""Have a stab at most files."""
if fname is not None and '.' in fname:
extension = fname.rsplit('.', 1)[1]
if extension in {'pdf', 'html', 'xml'}:
return False
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mcs07/ChemDataExtractor | chemdataextractor/reader/pdf.py | PdfReader._process_layout | def _process_layout(self, layout):
"""Process an LTPage layout and return a list of elements."""
# Here we just group text into paragraphs
elements = []
for lt_obj in layout:
if isinstance(lt_obj, LTTextBox) or isinstance(lt_obj, LTTextLine):
elements.append(P... | python | def _process_layout(self, layout):
"""Process an LTPage layout and return a list of elements."""
# Here we just group text into paragraphs
elements = []
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mcs07/ChemDataExtractor | chemdataextractor/text/__init__.py | get_encoding | def get_encoding(input_string, guesses=None, is_html=False):
"""Return the encoding of a byte string. Uses bs4 UnicodeDammit.
:param string input_string: Encoded byte string.
:param list[string] guesses: (Optional) List of encoding guesses to prioritize.
:param bool is_html: Whether the input is HTML.
... | python | def get_encoding(input_string, guesses=None, is_html=False):
"""Return the encoding of a byte string. Uses bs4 UnicodeDammit.
:param string input_string: Encoded byte string.
:param list[string] guesses: (Optional) List of encoding guesses to prioritize.
:param bool is_html: Whether the input is HTML.
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mcs07/ChemDataExtractor | chemdataextractor/text/__init__.py | levenshtein | def levenshtein(s1, s2, allow_substring=False):
"""Return the Levenshtein distance between two strings.
The Levenshtein distance (a.k.a "edit difference") is the number of characters that need to be substituted,
inserted or deleted to transform s1 into s2.
Setting the `allow_substring` parameter to Tr... | python | def levenshtein(s1, s2, allow_substring=False):
"""Return the Levenshtein distance between two strings.
The Levenshtein distance (a.k.a "edit difference") is the number of characters that need to be substituted,
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mcs07/ChemDataExtractor | chemdataextractor/text/__init__.py | bracket_level | def bracket_level(text, open={'(', '[', '{'}, close={')', ']', '}'}):
"""Return 0 if string contains balanced brackets or no brackets."""
level = 0
for c in text:
if c in open:
level += 1
elif c in close:
level -= 1
return level | python | def bracket_level(text, open={'(', '[', '{'}, close={')', ']', '}'}):
"""Return 0 if string contains balanced brackets or no brackets."""
level = 0
for c in text:
if c in open:
level += 1
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level -= 1
return level | [
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mcs07/ChemDataExtractor | chemdataextractor/cli/config.py | list | def list(ctx):
"""List all config values."""
log.debug('chemdataextractor.config.list')
for k in config:
click.echo('%s : %s' % (k, config[k])) | python | def list(ctx):
"""List all config values."""
log.debug('chemdataextractor.config.list')
for k in config:
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mcs07/ChemDataExtractor | chemdataextractor/cli/cem.py | train_crf | def train_crf(ctx, input, output, clusters):
"""Train CRF CEM recognizer."""
click.echo('chemdataextractor.crf.train')
sentences = []
for line in input:
sentence = []
for t in line.split():
token, tag, iob = t.rsplit('/', 2)
sentence.append(((token, tag), iob))
... | python | def train_crf(ctx, input, output, clusters):
"""Train CRF CEM recognizer."""
click.echo('chemdataextractor.crf.train')
sentences = []
for line in input:
sentence = []
for t in line.split():
token, tag, iob = t.rsplit('/', 2)
sentence.append(((token, tag), iob))
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mcs07/ChemDataExtractor | chemdataextractor/doc/text.py | Text.sentences | def sentences(self):
"""Return a list of Sentences that make up this text passage."""
sents = []
spans = self.sentence_tokenizer.span_tokenize(self.text)
for span in spans:
sent = Sentence(
text=self.text[span[0]:span[1]],
start=span[0],
... | python | def sentences(self):
"""Return a list of Sentences that make up this text passage."""
sents = []
spans = self.sentence_tokenizer.span_tokenize(self.text)
for span in spans:
sent = Sentence(
text=self.text[span[0]:span[1]],
start=span[0],
... | [
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mcs07/ChemDataExtractor | chemdataextractor/doc/text.py | Text.records | def records(self):
"""Return a list of records for this text passage."""
return ModelList(*[r for sent in self.sentences for r in sent.records]) | python | def records(self):
"""Return a list of records for this text passage."""
return ModelList(*[r for sent in self.sentences for r in sent.records]) | [
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mcs07/ChemDataExtractor | chemdataextractor/doc/text.py | Sentence.tokens | def tokens(self):
"""Return a list of token Spans for this sentence."""
spans = self.word_tokenizer.span_tokenize(self.text)
toks = [Token(
text=self.text[span[0]:span[1]],
start=span[0] + self.start,
end=span[1] + self.start,
lexicon=self.lexicon
... | python | def tokens(self):
"""Return a list of token Spans for this sentence."""
spans = self.word_tokenizer.span_tokenize(self.text)
toks = [Token(
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start=span[0] + self.start,
end=span[1] + self.start,
lexicon=self.lexicon
... | [
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mcs07/ChemDataExtractor | chemdataextractor/doc/text.py | Sentence.tags | def tags(self):
"""Return combined POS and NER tags."""
tags = self.pos_tags
for i, tag in enumerate(self.ner_tags):
if tag is not None:
tags[i] = tag
return tags | python | def tags(self):
"""Return combined POS and NER tags."""
tags = self.pos_tags
for i, tag in enumerate(self.ner_tags):
if tag is not None:
tags[i] = tag
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mcs07/ChemDataExtractor | chemdataextractor/doc/text.py | Sentence.records | def records(self):
"""Return a list of records for this sentence."""
compounds = ModelList()
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"""Return a list of records for this sentence."""
compounds = ModelList()
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mcs07/ChemDataExtractor | chemdataextractor/cli/chemdner.py | prepare_gold | def prepare_gold(ctx, annotations, gout):
"""Prepare bc-evaluate gold file from annotations supplied by CHEMDNER."""
click.echo('chemdataextractor.chemdner.prepare_gold')
for line in annotations:
pmid, ta, start, end, text, category = line.strip().split('\t')
gout.write('%s\t%s:%s:%s\n' % (p... | python | def prepare_gold(ctx, annotations, gout):
"""Prepare bc-evaluate gold file from annotations supplied by CHEMDNER."""
click.echo('chemdataextractor.chemdner.prepare_gold')
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pmid, ta, start, end, text, category = line.strip().split('\t')
gout.write('%s\t%s:%s:%s\n' % (p... | [
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mcs07/ChemDataExtractor | chemdataextractor/cli/chemdner.py | prepare_tokens | def prepare_tokens(ctx, input, annotations, tout, lout):
"""Prepare tokenized and tagged corpus file from those supplied by CHEMDNER."""
click.echo('chemdataextractor.chemdner.prepare_tokens')
# Collect the annotations into a dict
anndict = defaultdict(list)
for line in annotations:
pmid, ta... | python | def prepare_tokens(ctx, input, annotations, tout, lout):
"""Prepare tokenized and tagged corpus file from those supplied by CHEMDNER."""
click.echo('chemdataextractor.chemdner.prepare_tokens')
# Collect the annotations into a dict
anndict = defaultdict(list)
for line in annotations:
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mcs07/ChemDataExtractor | chemdataextractor/cli/chemdner.py | _prep_tags | def _prep_tags(t, annotations):
"""Apply IOB chemical entity tags and POS tags to text."""
tags = [['O' for _ in sent.tokens] for sent in t.sentences]
for start, end, text in annotations:
done_first = False
for i, sent in enumerate(t.sentences):
for j, token in enumerate(sent.tok... | python | def _prep_tags(t, annotations):
"""Apply IOB chemical entity tags and POS tags to text."""
tags = [['O' for _ in sent.tokens] for sent in t.sentences]
for start, end, text in annotations:
done_first = False
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mcs07/ChemDataExtractor | chemdataextractor/cli/pos.py | train_all | def train_all(ctx, output):
"""Train POS tagger on WSJ, GENIA, and both. With and without cluster features."""
click.echo('chemdataextractor.pos.train_all')
click.echo('Output: %s' % output)
ctx.invoke(train, output='%s_wsj_nocluster.pickle' % output, corpus='wsj', clusters=False)
ctx.invoke(train, ... | python | def train_all(ctx, output):
"""Train POS tagger on WSJ, GENIA, and both. With and without cluster features."""
click.echo('chemdataextractor.pos.train_all')
click.echo('Output: %s' % output)
ctx.invoke(train, output='%s_wsj_nocluster.pickle' % output, corpus='wsj', clusters=False)
ctx.invoke(train, ... | [
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mcs07/ChemDataExtractor | chemdataextractor/cli/pos.py | evaluate_all | def evaluate_all(ctx, model):
"""Evaluate POS taggers on WSJ and GENIA."""
click.echo('chemdataextractor.pos.evaluate_all')
click.echo('Model: %s' % model)
ctx.invoke(evaluate, model='%s_wsj_nocluster.pickle' % model, corpus='wsj', clusters=False)
ctx.invoke(evaluate, model='%s_wsj_nocluster.pickle'... | python | def evaluate_all(ctx, model):
"""Evaluate POS taggers on WSJ and GENIA."""
click.echo('chemdataextractor.pos.evaluate_all')
click.echo('Model: %s' % model)
ctx.invoke(evaluate, model='%s_wsj_nocluster.pickle' % model, corpus='wsj', clusters=False)
ctx.invoke(evaluate, model='%s_wsj_nocluster.pickle'... | [
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mcs07/ChemDataExtractor | chemdataextractor/cli/pos.py | train | def train(ctx, output, corpus, clusters):
"""Train POS Tagger."""
click.echo('chemdataextractor.pos.train')
click.echo('Output: %s' % output)
click.echo('Corpus: %s' % corpus)
click.echo('Clusters: %s' % clusters)
wsj_sents = []
genia_sents = []
if corpus == 'wsj' or corpus == 'wsj+gen... | python | def train(ctx, output, corpus, clusters):
"""Train POS Tagger."""
click.echo('chemdataextractor.pos.train')
click.echo('Output: %s' % output)
click.echo('Corpus: %s' % corpus)
click.echo('Clusters: %s' % clusters)
wsj_sents = []
genia_sents = []
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mcs07/ChemDataExtractor | chemdataextractor/cli/pos.py | evaluate | def evaluate(ctx, model, corpus, clusters):
"""Evaluate performance of POS Tagger."""
click.echo('chemdataextractor.pos.evaluate')
if corpus == 'wsj':
evaluation = wsj_evaluation
sents = list(evaluation.tagged_sents())
for i, wsj_sent in enumerate(sents):
sents[i] = [t fo... | python | def evaluate(ctx, model, corpus, clusters):
"""Evaluate performance of POS Tagger."""
click.echo('chemdataextractor.pos.evaluate')
if corpus == 'wsj':
evaluation = wsj_evaluation
sents = list(evaluation.tagged_sents())
for i, wsj_sent in enumerate(sents):
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mcs07/ChemDataExtractor | chemdataextractor/cli/pos.py | evaluate_perceptron | def evaluate_perceptron(ctx, model, corpus):
"""Evaluate performance of Averaged Perceptron POS Tagger."""
click.echo('chemdataextractor.pos.evaluate')
if corpus == 'wsj':
evaluation = wsj_evaluation
sents = list(evaluation.tagged_sents())
for i, wsj_sent in enumerate(sents):
... | python | def evaluate_perceptron(ctx, model, corpus):
"""Evaluate performance of Averaged Perceptron POS Tagger."""
click.echo('chemdataextractor.pos.evaluate')
if corpus == 'wsj':
evaluation = wsj_evaluation
sents = list(evaluation.tagged_sents())
for i, wsj_sent in enumerate(sents):
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mcs07/ChemDataExtractor | chemdataextractor/cli/pos.py | tag | def tag(ctx, input, output):
"""Output POS-tagged tokens."""
log.info('chemdataextractor.pos.tag')
log.info('Reading %s' % input.name)
doc = Document.from_file(input)
for element in doc.elements:
if isinstance(element, Text):
for sentence in element.sentences:
out... | python | def tag(ctx, input, output):
"""Output POS-tagged tokens."""
log.info('chemdataextractor.pos.tag')
log.info('Reading %s' % input.name)
doc = Document.from_file(input)
for element in doc.elements:
if isinstance(element, Text):
for sentence in element.sentences:
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mcs07/ChemDataExtractor | chemdataextractor/scrape/scraper.py | GetRequester.make_request | def make_request(self, session, url, **kwargs):
"""Make a HTTP GET request.
:param url: The URL to get.
:returns: The response to the request.
:rtype: requests.Response
"""
log.debug('Making request: GET %s %s' % (url, kwargs))
return session.get(url, **kwargs) | python | def make_request(self, session, url, **kwargs):
"""Make a HTTP GET request.
:param url: The URL to get.
:returns: The response to the request.
:rtype: requests.Response
"""
log.debug('Making request: GET %s %s' % (url, kwargs))
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mcs07/ChemDataExtractor | chemdataextractor/scrape/scraper.py | PostRequester.make_request | def make_request(self, session, url, **kwargs):
"""Make a HTTP POST request.
:param url: The URL to post to.
:param data: The data to post.
:returns: The response to the request.
:rtype: requests.Response
"""
log.debug('Making request: POST %s %s' % (url, kwargs)... | python | def make_request(self, session, url, **kwargs):
"""Make a HTTP POST request.
:param url: The URL to post to.
:param data: The data to post.
:returns: The response to the request.
:rtype: requests.Response
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mcs07/ChemDataExtractor | chemdataextractor/scrape/scraper.py | UrlScraper.run | def run(self, url):
"""Request URL, scrape response and return an EntityList."""
url = self.process_url(url)
if not url:
return
response = self.make_request(self.http, url)
selector = self.process_response(response)
entities = []
for root in self.get_r... | python | def run(self, url):
"""Request URL, scrape response and return an EntityList."""
url = self.process_url(url)
if not url:
return
response = self.make_request(self.http, url)
selector = self.process_response(response)
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mcs07/ChemDataExtractor | chemdataextractor/scrape/clean.py | Cleaner.clean_html | def clean_html(self, html):
"""Apply ``Cleaner`` to HTML string or document and return a cleaned string or document."""
result_type = type(html)
if isinstance(html, six.string_types):
doc = html_fromstring(html)
else:
doc = copy.deepcopy(html)
self(doc)
... | python | def clean_html(self, html):
"""Apply ``Cleaner`` to HTML string or document and return a cleaned string or document."""
result_type = type(html)
if isinstance(html, six.string_types):
doc = html_fromstring(html)
else:
doc = copy.deepcopy(html)
self(doc)
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mcs07/ChemDataExtractor | chemdataextractor/scrape/clean.py | Cleaner.clean_markup | def clean_markup(self, markup, parser=None):
"""Apply ``Cleaner`` to markup string or document and return a cleaned string or document."""
result_type = type(markup)
if isinstance(markup, six.string_types):
doc = fromstring(markup, parser=parser)
else:
doc = copy.... | python | def clean_markup(self, markup, parser=None):
"""Apply ``Cleaner`` to markup string or document and return a cleaned string or document."""
result_type = type(markup)
if isinstance(markup, six.string_types):
doc = fromstring(markup, parser=parser)
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mcs07/ChemDataExtractor | chemdataextractor/text/processors.py | floats | def floats(s):
"""Convert string to float. Handles more string formats that the standard python conversion."""
try:
return float(s)
except ValueError:
s = re.sub(r'(\d)\s*\(\d+(\.\d+)?\)', r'\1', s) # Remove bracketed numbers from end
s = re.sub(r'(\d)\s*±\s*\d+(\.\d+)?', r'\1... | python | def floats(s):
"""Convert string to float. Handles more string formats that the standard python conversion."""
try:
return float(s)
except ValueError:
s = re.sub(r'(\d)\s*\(\d+(\.\d+)?\)', r'\1', s) # Remove bracketed numbers from end
s = re.sub(r'(\d)\s*±\s*\d+(\.\d+)?', r'\1... | [
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mcs07/ChemDataExtractor | chemdataextractor/text/processors.py | strip_querystring | def strip_querystring(url):
"""Remove the querystring from the end of a URL."""
p = six.moves.urllib.parse.urlparse(url)
return p.scheme + "://" + p.netloc + p.path | python | def strip_querystring(url):
"""Remove the querystring from the end of a URL."""
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linuxsoftware/ls.joyous | ls/joyous/utils/telltime.py | getLocalTime | def getLocalTime(date, time, *args, **kwargs):
"""
Get the time in the local timezone from date and time
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if time is not None:
return getLocalDateAndTime(date, time, *args, **kwargs)[1] | python | def getLocalTime(date, time, *args, **kwargs):
"""
Get the time in the local timezone from date and time
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Get the date and time in the local timezone from date and optionally time
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linuxsoftware/ls.joyous | ls/joyous/utils/telltime.py | getLocalDatetime | def getLocalDatetime(date, time, tz=None, timeDefault=dt.time.max):
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Get a datetime in the local timezone from date and optionally time
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localTZ = timezone.get_current_timezone()
if tz is None or tz == localTZ:
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#... | python | def getLocalDatetime(date, time, tz=None, timeDefault=dt.time.max):
"""
Get a datetime in the local timezone from date and optionally time
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localTZ = timezone.get_current_timezone()
if tz is None or tz == localTZ:
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linuxsoftware/ls.joyous | ls/joyous/utils/telltime.py | getAwareDatetime | def getAwareDatetime(date, time, tz, timeDefault=dt.time.max):
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Get a datetime in the given timezone from date and optionally time.
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if time is None:
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Get a datetime in the given timezone from date and optionally time.
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linuxsoftware/ls.joyous | ls/joyous/utils/weeks.py | _iso_num_weeks | def _iso_num_weeks(iso_year):
"Get the number of ISO-weeks in this year"
year_start = _iso_year_start(iso_year)
next_year_start = _iso_year_start(iso_year+1)
year_num_weeks = ((next_year_start - year_start).days) // 7
return year_num_weeks | python | def _iso_num_weeks(iso_year):
"Get the number of ISO-weeks in this year"
year_start = _iso_year_start(iso_year)
next_year_start = _iso_year_start(iso_year+1)
year_num_weeks = ((next_year_start - year_start).days) // 7
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linuxsoftware/ls.joyous | ls/joyous/utils/weeks.py | _iso_info | def _iso_info(iso_year, iso_week):
"Give all the iso info we need from one calculation"
prev_year_start = _iso_year_start(iso_year-1)
year_start = _iso_year_start(iso_year)
next_year_start = _iso_year_start(iso_year+1)
first_day = year_start + dt.timedelta(weeks=iso_week-1)
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prev_year_start = _iso_year_start(iso_year-1)
year_start = _iso_year_start(iso_year)
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linuxsoftware/ls.joyous | ls/joyous/utils/weeks.py | _iso_week_of_month | def _iso_week_of_month(date_value):
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weekday_of_first = date_value.replace(day=1).weekday()
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linuxsoftware/ls.joyous | ls/joyous/utils/weeks.py | _ssweek_year_start | def _ssweek_year_start(ssweek_year):
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fifth_jan = dt.date(ssweek_year, 1, 5)
delta = dt.timedelta(fifth_jan.weekday()+1)
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"The gregorian calendar date of the first day of the given Sundaystarting-week year"
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linuxsoftware/ls.joyous | ls/joyous/utils/weeks.py | _ssweek_to_gregorian | def _ssweek_to_gregorian(ssweek_year, ssweek_week, ssweek_day):
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year_start = _ssweek_year_start(ssweek_year)
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linuxsoftware/ls.joyous | ls/joyous/utils/weeks.py | _ssweek_num_weeks | def _ssweek_num_weeks(ssweek_year):
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year_start = _ssweek_year_start(ssweek_year)
next_year_start = _ssweek_year_start(ssweek_year+1)
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linuxsoftware/ls.joyous | ls/joyous/utils/weeks.py | _ssweek_info | def _ssweek_info(ssweek_year, ssweek_week):
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yearStart = _ssweek_year_start(date_value.year)
weekNum = ((date_value - yearStart).days) // 7 + 1
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linuxsoftware/ls.joyous | ls/joyous/utils/weeks.py | _ssweek_of_month | def _ssweek_of_month(date_value):
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weekday_of_first = (date_value.replace(day=1).weekday() + 1) % 7
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linuxsoftware/ls.joyous | ls/joyous/utils/recurrence.py | Recurrence.bymonthday | def bymonthday(self):
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"""
The month days where the recurrence will be applied.
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retval = []
if self.rule._bymonthday:
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage.routeDefault | def routeDefault(self, request, year=None):
"""Route a request to the default calendar view."""
eventsView = request.GET.get('view', self.default_view)
if eventsView in ("L", "list"):
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"""Route a request to the default calendar view."""
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage.routeByMonthAbbr | def routeByMonthAbbr(self, request, year, monthAbbr):
"""Route a request with a month abbreviation to the monthly view."""
month = (DatePictures['Mon'].index(monthAbbr.lower()) // 4) + 1
return self.serveMonth(request, year, month) | python | def routeByMonthAbbr(self, request, year, monthAbbr):
"""Route a request with a month abbreviation to the monthly view."""
month = (DatePictures['Mon'].index(monthAbbr.lower()) // 4) + 1
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage.serveMonth | def serveMonth(self, request, year=None, month=None):
"""Monthly calendar view."""
myurl = self.get_url(request)
def myUrl(urlYear, urlMonth):
if 1900 <= urlYear <= 2099:
return myurl + self.reverse_subpage('serveMonth',
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"""Monthly calendar view."""
myurl = self.get_url(request)
def myUrl(urlYear, urlMonth):
if 1900 <= urlYear <= 2099:
return myurl + self.reverse_subpage('serveMonth',
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage.serveWeek | def serveWeek(self, request, year=None, week=None):
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myurl = self.get_url(request)
def myUrl(urlYear, urlWeek):
if (urlYear < 1900 or
urlYear > 2099 or
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"""Weekly calendar view."""
myurl = self.get_url(request)
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if (urlYear < 1900 or
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage.serveDay | def serveDay(self, request, year=None, month=None, dom=None):
"""The events of the day list view."""
myurl = self.get_url(request)
today = timezone.localdate()
if year is None: year = today.year
if month is None: month = today.month
if dom is None: dom = today.day
... | python | def serveDay(self, request, year=None, month=None, dom=None):
"""The events of the day list view."""
myurl = self.get_url(request)
today = timezone.localdate()
if year is None: year = today.year
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if dom is None: dom = today.day
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage.serveUpcoming | def serveUpcoming(self, request):
"""Upcoming events list view."""
myurl = self.get_url(request)
today = timezone.localdate()
monthlyUrl = myurl + self.reverse_subpage('serveMonth',
args=[today.year, today.month])
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"""Upcoming events list view."""
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage.serveMiniMonth | def serveMiniMonth(self, request, year=None, month=None):
"""Serve data for the MiniMonth template tag."""
if not request.is_ajax():
raise Http404("/mini/ is for ajax requests only")
today = timezone.localdate()
if year is None: year = today.year
if month is None: mo... | python | def serveMiniMonth(self, request, year=None, month=None):
"""Serve data for the MiniMonth template tag."""
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage._allowAnotherAt | def _allowAnotherAt(cls, parent):
"""You can only create one of these pages per site."""
site = parent.get_site()
if site is None:
return False
return not cls.peers().descendant_of(site.root_page).exists() | python | def _allowAnotherAt(cls, parent):
"""You can only create one of these pages per site."""
site = parent.get_site()
if site is None:
return False
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage.peers | def peers(cls):
"""Return others of the same concrete type."""
contentType = ContentType.objects.get_for_model(cls)
return cls.objects.filter(content_type=contentType) | python | def peers(cls):
"""Return others of the same concrete type."""
contentType = ContentType.objects.get_for_model(cls)
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage._getEventsOnDay | def _getEventsOnDay(self, request, day):
"""Return all the events in this site for a given day."""
home = request.site.root_page
return getAllEventsByDay(request, day, day, home=home)[0] | python | def _getEventsOnDay(self, request, day):
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage._getEventsByDay | def _getEventsByDay(self, request, firstDay, lastDay):
"""
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"""
home = request.site.root_page
return getAllEventsByDay(request, firstDay, lastDay, home=home) | python | def _getEventsByDay(self, request, firstDay, lastDay):
"""
Return the events in this site for the dates given, grouped by day.
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage._getEventsByWeek | def _getEventsByWeek(self, request, year, month):
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home = request.site.root_page
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage._getUpcomingEvents | def _getUpcomingEvents(self, request):
"""Return the upcoming events in this site."""
home = request.site.root_page
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"""Return the upcoming events in this site."""
home = request.site.root_page
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage._getPastEvents | def _getPastEvents(self, request):
"""Return the past events in this site."""
home = request.site.root_page
return getAllPastEvents(request, home=home) | python | def _getPastEvents(self, request):
"""Return the past events in this site."""
home = request.site.root_page
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage._getEventFromUid | def _getEventFromUid(self, request, uid):
"""Try and find an event with the given UID in this site."""
event = getEventFromUid(request, uid) # might raise ObjectDoesNotExist
home = request.site.root_page
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"""Try and find an event with the given UID in this site."""
event = getEventFromUid(request, uid) # might raise ObjectDoesNotExist
home = request.site.root_page
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | CalendarPage._getAllEvents | def _getAllEvents(self, request):
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"""Return all the events in this site."""
home = request.site.root_page
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | SpecificCalendarPage._getEventsOnDay | def _getEventsOnDay(self, request, day):
"""Return my child events for a given day."""
return getAllEventsByDay(request, day, day, home=self)[0] | python | def _getEventsOnDay(self, request, day):
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | SpecificCalendarPage._getEventsByDay | def _getEventsByDay(self, request, firstDay, lastDay):
"""
Return my child events for the dates given, grouped by day.
"""
return getAllEventsByDay(request, firstDay, lastDay, home=self) | python | def _getEventsByDay(self, request, firstDay, lastDay):
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Return my child events for the dates given, grouped by day.
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | SpecificCalendarPage._getEventsByWeek | def _getEventsByWeek(self, request, year, month):
"""Return my child events for the given month grouped by week."""
return getAllEventsByWeek(request, year, month, home=self) | python | def _getEventsByWeek(self, request, year, month):
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linuxsoftware/ls.joyous | ls/joyous/models/calendar.py | SpecificCalendarPage._getEventFromUid | def _getEventFromUid(self, request, uid):
"""Try and find a child event with the given UID."""
event = getEventFromUid(request, uid)
if event.get_ancestors().filter(id=self.id).exists():
# only return event if it is a descendant
return event | python | def _getEventFromUid(self, request, uid):
"""Try and find a child event with the given UID."""
event = getEventFromUid(request, uid)
if event.get_ancestors().filter(id=self.id).exists():
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linuxsoftware/ls.joyous | ls/joyous/templatetags/joyous_tags.py | events_this_week | def events_this_week(context):
"""
Displays a week's worth of events. Starts week with Monday, unless today is Sunday.
"""
request = context['request']
home = request.site.root_page
cal = CalendarPage.objects.live().descendant_of(home).first()
calUrl = cal.get_url(request) if cal else None... | python | def events_this_week(context):
"""
Displays a week's worth of events. Starts week with Monday, unless today is Sunday.
"""
request = context['request']
home = request.site.root_page
cal = CalendarPage.objects.live().descendant_of(home).first()
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linuxsoftware/ls.joyous | ls/joyous/templatetags/joyous_tags.py | minicalendar | def minicalendar(context):
"""
Displays a little ajax version of the calendar.
"""
today = dt.date.today()
request = context['request']
home = request.site.root_page
cal = CalendarPage.objects.live().descendant_of(home).first()
calUrl = cal.get_url(request) if cal else None
if cal:
... | python | def minicalendar(context):
"""
Displays a little ajax version of the calendar.
"""
today = dt.date.today()
request = context['request']
home = request.site.root_page
cal = CalendarPage.objects.live().descendant_of(home).first()
calUrl = cal.get_url(request) if cal else None
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linuxsoftware/ls.joyous | ls/joyous/templatetags/joyous_tags.py | subsite_upcoming_events | def subsite_upcoming_events(context):
"""
Displays a list of all upcoming events in this site.
"""
request = context['request']
home = request.site.root_page
return {'request': request,
'events': getAllUpcomingEvents(request, home=home)} | python | def subsite_upcoming_events(context):
"""
Displays a list of all upcoming events in this site.
"""
request = context['request']
home = request.site.root_page
return {'request': request,
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linuxsoftware/ls.joyous | ls/joyous/templatetags/joyous_tags.py | group_upcoming_events | def group_upcoming_events(context, group=None):
"""
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group. If the group is not specified it is assumed to be the current page.
"""
request = context.get('request')
if group is None:
group = context.get('page')
if... | python | def group_upcoming_events(context, group=None):
"""
Displays a list of all upcoming events that are assigned to a specific
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"""
request = context.get('request')
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linuxsoftware/ls.joyous | ls/joyous/templatetags/joyous_tags.py | next_on | def next_on(context, rrevent=None):
"""
Displays when the next occurence of a recurring event will be. If the
recurring event is not specified it is assumed to be the current page.
"""
request = context['request']
if rrevent is None:
rrevent = context.get('page')
eventNextOn = getat... | python | def next_on(context, rrevent=None):
"""
Displays when the next occurence of a recurring event will be. If the
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request = context['request']
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linuxsoftware/ls.joyous | ls/joyous/templatetags/joyous_tags.py | location_gmap | def location_gmap(context, location):
"""Display a link to Google maps iff we are using WagtailGMaps"""
gmapq = None
if getattr(MapFieldPanel, "UsingWagtailGMaps", False):
gmapq = location
return {'gmapq': gmapq} | python | def location_gmap(context, location):
"""Display a link to Google maps iff we are using WagtailGMaps"""
gmapq = None
if getattr(MapFieldPanel, "UsingWagtailGMaps", False):
gmapq = location
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linuxsoftware/ls.joyous | ls/joyous/models/events.py | getGroupUpcomingEvents | def getGroupUpcomingEvents(request, group):
"""
Return all the upcoming events that are assigned to the specified group.
:param request: Django request object
:param group: for this group page
:rtype: list of the namedtuple ThisEvent (title, page, url)
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"""
Return all the upcoming events that are assigned to the specified group.
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:rtype: list of the namedtuple ThisEvent (title, page, url)
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linuxsoftware/ls.joyous | ls/joyous/models/events.py | EventBase.group | def group(self):
"""
The group this event belongs to. Adding the event as a child of a
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"""
retval = None
parent = self.get_parent()
Group = get_group_model()
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"""
The group this event belongs to. Adding the event as a child of a
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retval = None
parent = self.get_parent()
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linuxsoftware/ls.joyous | ls/joyous/models/events.py | EventBase.isAuthorized | def isAuthorized(self, request):
"""
Is the user authorized for the requested action with this event?
"""
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if restrictions and request is None:
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"""
Is the user authorized for the requested action with this event?
"""
restrictions = self.get_view_restrictions()
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linuxsoftware/ls.joyous | ls/joyous/models/events.py | RecurringEventPage._upcoming_datetime_from | def _upcoming_datetime_from(self):
"""
The datetime this event next starts in the local time zone, or None if
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"""
nextDt = self.__localAfter(timezone.localtime(), dt.time.max,
excludeCancellations=True,
... | python | def _upcoming_datetime_from(self):
"""
The datetime this event next starts in the local time zone, or None if
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"""
nextDt = self.__localAfter(timezone.localtime(), dt.time.max,
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] | 316283140ca5171a68ad3170a5964fdc89be0b56 | https://github.com/linuxsoftware/ls.joyous/blob/316283140ca5171a68ad3170a5964fdc89be0b56/ls/joyous/models/events.py#L961-L969 | train |
linuxsoftware/ls.joyous | ls/joyous/models/events.py | RecurringEventPage._past_datetime_from | def _past_datetime_from(self):
"""
The datetime this event previously started in the local time zone, or
None if it never did.
"""
prevDt = self.__localBefore(timezone.localtime(), dt.time.max,
excludeCancellations=True,
... | python | def _past_datetime_from(self):
"""
The datetime this event previously started in the local time zone, or
None if it never did.
"""
prevDt = self.__localBefore(timezone.localtime(), dt.time.max,
excludeCancellations=True,
... | [
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linuxsoftware/ls.joyous | ls/joyous/models/events.py | RecurringEventPage._first_datetime_from | def _first_datetime_from(self):
"""
The datetime this event first started in the local time zone, or None if
it never did.
"""
myFromDt = self._getMyFirstDatetimeFrom()
localTZ = timezone.get_current_timezone()
return myFromDt.astimezone(localTZ) | python | def _first_datetime_from(self):
"""
The datetime this event first started in the local time zone, or None if
it never did.
"""
myFromDt = self._getMyFirstDatetimeFrom()
localTZ = timezone.get_current_timezone()
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linuxsoftware/ls.joyous | ls/joyous/models/events.py | RecurringEventPage._getFromTime | def _getFromTime(self, atDate=None):
"""
What was the time of this event? Due to time zones that depends what
day we are talking about. If no day is given, assume today.
"""
if atDate is None:
atDate = timezone.localdate(timezone=self.tz)
return getLocalTime... | python | def _getFromTime(self, atDate=None):
"""
What was the time of this event? Due to time zones that depends what
day we are talking about. If no day is given, assume today.
"""
if atDate is None:
atDate = timezone.localdate(timezone=self.tz)
return getLocalTime... | [
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linuxsoftware/ls.joyous | ls/joyous/models/events.py | RecurringEventPage._getFromDt | def _getFromDt(self):
"""
Get the datetime of the next event after or before now.
"""
myNow = timezone.localtime(timezone=self.tz)
return self.__after(myNow) or self.__before(myNow) | python | def _getFromDt(self):
"""
Get the datetime of the next event after or before now.
"""
myNow = timezone.localtime(timezone=self.tz)
return self.__after(myNow) or self.__before(myNow) | [
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linuxsoftware/ls.joyous | ls/joyous/models/events.py | RecurringEventPage._futureExceptions | def _futureExceptions(self, request):
"""
Returns all future extra info, cancellations and postponements created
for this recurring event
"""
retval = []
# We know all future exception dates are in the parent time zone
myToday = timezone.localdate(timezone=self.tz... | python | def _futureExceptions(self, request):
"""
Returns all future extra info, cancellations and postponements created
for this recurring event
"""
retval = []
# We know all future exception dates are in the parent time zone
myToday = timezone.localdate(timezone=self.tz... | [
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