code string | signature string | docstring string | loss_without_docstring float64 | loss_with_docstring float64 | factor float64 |
|---|---|---|---|---|---|
l = []
E = ElementMaker(namespace="http://ilk.uvt.nl/folia",nsmap={None: "http://ilk.uvt.nl/folia", 'xml' : "http://www.w3.org/XML/1998/namespace"})
for annotationtype, set in self.annotations:
label = None
#Find the 'label' for the declarations dynamically (aka... | def xmldeclarations(self) | Internal method to generate XML nodes for all declarations | 3.918028 | 3.828393 | 1.023413 |
l = []
for annotationtype, set in self.annotations:
label = None
#Find the 'label' for the declarations dynamically (aka: AnnotationType --> String)
for key, value in vars(AnnotationType).items():
if value == annotationtype:
... | def jsondeclarations(self) | Return all declarations in a form ready to be serialised to JSON.
Returns:
list of dict | 5.013553 | 5.123099 | 0.978617 |
self.pendingvalidation()
E = ElementMaker(namespace="http://ilk.uvt.nl/folia",nsmap={'xml' : "http://www.w3.org/XML/1998/namespace", 'xlink':"http://www.w3.org/1999/xlink"})
attribs = {}
attribs['{http://www.w3.org/XML/1998/namespace}id'] = self.id
#if self.version:
... | def xml(self) | Serialise the document to XML.
Returns:
lxml.etree.Element
See also:
:meth:`Document.xmlstring` | 4.15994 | 4.183474 | 0.994375 |
self.pendingvalidation()
jsondoc = {'id': self.id, 'children': [], 'declarations': self.jsondeclarations() }
if self.version:
jsondoc['version'] = self.version
else:
jsondoc['version'] = FOLIAVERSION
jsondoc['generator'] = 'pynlpl.formats.folia-v... | def json(self) | Serialise the document to a ``dict`` ready for serialisation to JSON.
Example::
import json
jsondoc = json.dumps(doc.json()) | 7.851553 | 7.921583 | 0.99116 |
E = ElementMaker(namespace="http://ilk.uvt.nl/folia",nsmap={None: "http://ilk.uvt.nl/folia", 'xml' : "http://www.w3.org/XML/1998/namespace"})
elements = []
if self.metadatatype == "native":
if isinstance(self.metadata, NativeMetaData):
for key, value in self.... | def xmlmetadata(self) | Internal method to serialize metadata to XML | 2.635773 | 2.61233 | 1.008974 |
self.metadata = ElementTree.tostring(node, xml_declaration=False, pretty_print=True, encoding='utf-8')
else:
self.metadata = ElementTree.tostring(node, encoding='utf-8')
n = node.xpath('imdi:Session/imdi:Title', namespaces=ns)
if n and n[0].text: self._title = n[0].text
... | def setimdi(self, node): #OBSOLETE
ns = {'imdi': 'http://www.mpi.nl/IMDI/Schema/IMDI'}
self.metadatatype = MetaDataType.IMDI
if LXE | OBSOLETE | 1.884285 | 1.86903 | 1.008162 |
if (sys.version > '3' and not isinstance(set,str)) or (sys.version < '3' and not isinstance(set,(str,unicode))):
raise ValueError("Set parameter for declare() must be a string")
if inspect.isclass(annotationtype):
annotationtype = annotationtype.ANNOTATIONTYPE
i... | def declare(self, annotationtype, set, **kwargs) | Declare a new annotation type to be used in the document.
Keyword arguments can be used to set defaults for any annotation of this type and set.
Arguments:
annotationtype: The type of annotation, this is conveyed by passing the corresponding annototion class (such as :class:`PosAnnotation`... | 2.33462 | 2.340233 | 0.997601 |
if inspect.isclass(annotationtype): annotationtype = annotationtype.ANNOTATIONTYPE
return ( (annotationtype,set) in self.annotations) or (set in self.alias_set and self.alias_set[set] and (annotationtype, self.alias_set[set]) in self.annotations ) | def declared(self, annotationtype, set) | Checks if the annotation type is present (i.e. declared) in the document.
Arguments:
annotationtype: The type of annotation, this is conveyed by passing the corresponding annototion class (such as :class:`PosAnnotation` for example), or a member of :class:`AnnotationType`, such as ``AnnotationType.... | 4.291375 | 4.896905 | 0.876344 |
if inspect.isclass(annotationtype) or isinstance(annotationtype,AbstractElement): annotationtype = annotationtype.ANNOTATIONTYPE
try:
return list(self.annotationdefaults[annotationtype].keys())[0]
except KeyError:
raise NoDefaultError
except IndexError:
... | def defaultset(self, annotationtype) | Obtain the default set for the specified annotation type.
Arguments:
annotationtype: The type of annotation, this is conveyed by passing the corresponding annototion class (such as :class:`PosAnnotation` for example), or a member of :class:`AnnotationType`, such as ``AnnotationType.POS``.
... | 5.508179 | 4.490763 | 1.226558 |
if inspect.isclass(annotationtype) or isinstance(annotationtype,AbstractElement): annotationtype = annotationtype.ANNOTATIONTYPE
if not set: set = self.defaultset(annotationtype)
try:
return self.annotationdefaults[annotationtype][set]['annotator']
except KeyError:
... | def defaultannotator(self, annotationtype, set=None) | Obtain the default annotator for the specified annotation type and set.
Arguments:
annotationtype: The type of annotation, this is conveyed by passing the corresponding annototion class (such as :class:`PosAnnotation` for example), or a member of :class:`AnnotationType`, such as ``AnnotationType.PO... | 5.30407 | 4.196514 | 1.263923 |
if not (value is None):
if (self.metadatatype == "native"):
self.metadata['title'] = value
else:
self._title = value
if (self.metadatatype == "native"):
if 'title' in self.metadata:
return self.metadata['title']... | def title(self, value=None) | Get or set the document's title from/in the metadata
No arguments: Get the document's title from metadata
Argument: Set the document's title in metadata | 2.877156 | 2.896225 | 0.993416 |
if not (value is None):
if (self.metadatatype == "native"):
self.metadata['date'] = value
else:
self._date = value
if (self.metadatatype == "native"):
if 'date' in self.metadata:
return self.metadata['date']
... | def date(self, value=None) | Get or set the document's date from/in the metadata.
No arguments: Get the document's date from metadata
Argument: Set the document's date in metadata | 2.998534 | 2.909766 | 1.030507 |
if not (value is None):
if (self.metadatatype == "native"):
self.metadata['publisher'] = value
else:
self._publisher = value
if (self.metadatatype == "native"):
if 'publisher' in self.metadata:
return self.metad... | def publisher(self, value=None) | No arguments: Get the document's publisher from metadata
Argument: Set the document's publisher in metadata | 2.960265 | 2.717883 | 1.08918 |
if not (value is None):
if (self.metadatatype == "native"):
self.metadata['license'] = value
else:
self._license = value
if (self.metadatatype == "native"):
if 'license' in self.metadata:
return self.metadata['l... | def license(self, value=None) | No arguments: Get the document's license from metadata
Argument: Set the document's license in metadata | 2.952225 | 2.726532 | 1.082777 |
if not (value is None):
if (self.metadatatype == "native"):
self.metadata['language'] = value
else:
self._language = value
if self.metadatatype == "native":
if 'language' in self.metadata:
return self.metadata['... | def language(self, value=None) | No arguments: Get the document's language (ISO-639-3) from metadata
Argument: Set the document's language (ISO-639-3) in metadata | 3.051805 | 2.833565 | 1.07702 |
if 'type' in node.attrib:
self.metadatatype = node.attrib['type']
else:
#no type specified, default to native
self.metadatatype = "native"
if 'src' in node.attrib:
self.metadata = ExternalMetaData(node.attrib['src'])
elif self.me... | def parsemetadata(self, node) | Internal method to parse metadata | 3.4689 | 3.450739 | 1.005263 |
if self.debug: print("[PyNLPl FoLiA DEBUG] Processing pending validations (if any)",file=stderr)
if warnonly is None and self and self.version:
warnonly = (checkversion(self.version, '1.5.0') < 0) #warn only for documents older than FoLiA v1.5
if self.textvalidation:
... | def pendingvalidation(self, warnonly=None) | Perform any pending validations
Parameters:
warnonly (bool): Warn only (True) or raise exceptions (False). If set to None then this value will be determined based on the document's FoLiA version (Warn only before FoLiA v1.5)
Returns:
bool | 6.249314 | 5.690001 | 1.098298 |
if self.mode == Mode.MEMORY:
for t in self.data:
if Class.__name__ == 'Text':
yield t
else:
for e in t.select(Class,set,recursive,ignore):
yield e | def select(self, Class, set=None, recursive=True, ignore=True) | See :meth:`AbstractElement.select` | 5.078865 | 4.814737 | 1.054858 |
if self.mode == Mode.MEMORY:
s = 0
for t in self.data:
s += sum( 1 for e in t.select(Class,recursive,True ) )
return s | def count(self, Class, set=None, recursive=True,ignore=True) | See :meth:`AbstractElement.count` | 8.376006 | 7.993842 | 1.047807 |
if index is None:
return self.select(Paragraph)
else:
if index < 0:
index = sum(t.count(Paragraph) for t in self.data) + index
for t in self.data:
for i,e in enumerate(t.select(Paragraph)) :
if i == index:
... | def paragraphs(self, index = None) | Return a generator of all paragraphs found in the document.
If an index is specified, return the n'th paragraph only (starting at 0) | 3.667985 | 3.669436 | 0.999605 |
if index is None:
return self.select(Sentence,None,True,[Quote])
else:
if index < 0:
index = sum(t.count(Sentence,None,True,[Quote]) for t in self.data) + index
for t in self.data:
for i,e in enumerate(t.select(Sentence,None,Tr... | def sentences(self, index = None) | Return a generator of all sentence found in the document. Except for sentences in quotes.
If an index is specified, return the n'th sentence only (starting at 0) | 4.06069 | 3.785156 | 1.072793 |
#backward compatibility, old versions didn't have cls as first argument, so if a boolean is passed first we interpret it as the 2nd:
if cls is True or cls is False:
retaintokenisation = cls
cls = 'current'
s = ""
for c in self.data:
if s: s ... | def text(self, cls='current', retaintokenisation=False) | Returns the text of the entire document (returns a unicode instance)
See also:
:meth:`AbstractElement.text` | 5.648828 | 5.998115 | 0.941767 |
if not nextstate in processedstates:
self._states(nextstate, processedstates)
for _, nextstate in state.transitions:
if not nextstate in processedstates:
self._states(nextstate, processedstates)
return processedstates | def _states(self, state, processedstates=[]): #pylint: disable=dangerous-default-value
processedstates.append(state)
for nextstate in state.epsilon | Iterate over all states in no particular order | 3.301553 | 2.324134 | 1.420552 |
if 'debug' in kwargs:
if 'currentdebug' in kwargs:
if kwargs['currentdebug'] < kwargs['debug']:
return False
else:
return False #no currentdebug passed, assuming no debug mode and thus skipping message
s = "[" + datetime.datetime.now().strftime("%Y-%... | def log(msg, **kwargs) | Generic log method. Will prepend timestamp.
Keyword arguments:
system - Name of the system/module
indent - Integer denoting the desired level of indentation
streams - List of streams to output to
stream - Stream to output to (singleton version of streams) | 3.350699 | 3.146059 | 1.065047 |
finalsolution = None
bestscore = None
for solution in self:
if bestscore == None:
bestscore = solution.score()
finalsolution = solution
elif self.minimize:
score = solution.score()
if score < bestsco... | def searchbest(self) | Returns the single best result (if multiple have the same score, the first match is returned) | 2.211629 | 2.082187 | 1.062166 |
solutions = PriorityQueue([], lambda x: x.score, self.minimize, length=n, blockworse=False, blockequal=False,duplicates=False)
for solution in self:
solutions.append(solution)
return solutions | def searchtop(self,n=10) | Return the top n best resulta (or possibly less if not enough is found) | 17.739511 | 15.993224 | 1.109189 |
solutions = deque([], n)
for solution in self:
solutions.append(solution)
return solutions | def searchlast(self,n=10) | Return the last n results (or possibly less if not found). Note that the last results are not necessarily the best ones! Depending on the search type. | 9.863415 | 8.865089 | 1.112613 |
if not isinstance(lemma,unicode):
lemma = unicode(lemma,'utf-8')
http, resp, content = self.connect()
params = ""
fragment = ""
path = "cdb_syn"
if self.debug:
printf( "cornettodb/views/query_remote_syn_lemma: db_opt: %s" % path )
... | def get_syn_ids_by_lemma(self, lemma) | Returns a list of synset IDs based on a lemma | 3.831795 | 3.827914 | 1.001014 |
http, resp, content = self.connect()
params = ""
fragment = ""
path = "cdb_syn"
if self.debug:
printf( "cornettodb/views/query_remote_syn_id: db_opt: %s" % path )
# output_opt: plain, html, xml
# 'xml' is actually xhtml (with markup), bu... | def get_synset_xml(self,syn_id) | call cdb_syn with synset identifier -> returns the synset xml; | 3.823879 | 3.731251 | 1.024825 |
root = self.get_synset_xml(syn_id)
elem_synonyms = root.find( ".//synonyms" )
lus = []
for elem_synonym in elem_synonyms:
synonym_str = elem_synonym.get( "c_lu_id-previewtext" ) # get "c_lu_id-previewtext" attribute
# synonym_str ends with ":<nu... | def get_lus_from_synset(self, syn_id) | Returns a list of (word, lu_id) tuples given a synset ID | 4.913917 | 4.496503 | 1.092831 |
if not lemma:
return self.get_lus_from_synset(syn_id) #alias
if not isinstance(lemma,unicode):
lemma = unicode(lemma,'utf-8')
root = self.get_synset_xml(syn_id)
elem_synonyms = root.find( ".//synonyms" )
lu_id = None
synonyms = []
... | def get_lu_from_synset(self, syn_id, lemma = None) | Returns (lu_id, synonyms=[(word, lu_id)] ) tuple given a synset ID and a lemma | 3.56635 | 3.245774 | 1.098767 |
l = []
for word_id, senses,distance in self:
for sense, confidence in senses:
if not sense in l: l.append(sense)
if bestonly:
break
return l | def senses(self, bestonly=False) | Returns a list of all predicted senses | 5.897015 | 5.76519 | 1.022866 |
if isinstance(input_data, list) or isinstance(input_data, tuple):
input_data = " ".join(input_data)
input_data = u(input_data, source_encoding) #decode (or preferably do this in an earlier stage)
input_data = input_data.strip(' \t\n')
s = input_data.encode(self.s... | def process(self,input_data, source_encoding="utf-8", return_unicode = True, oldfrog=False) | Receives input_data in the form of a str or unicode object, passes this to the server, with proper consideration for the encodings, and returns the Frog output as a list of tuples: (word,pos,lemma,morphology), each of these is a proper unicode object unless return_unicode is set to False, in which case raw strings will... | 3.473105 | 3.278679 | 1.0593 |
alignment = []
cursor = 0
for inputword in inputwords:
if len(outputwords) > cursor and outputwords[cursor] == inputword:
alignment.append(cursor)
cursor += 1
elif len(outputwords) > cursor+1 and outputwords[cursor+1] == inputword:... | def align(self,inputwords, outputwords) | For each inputword, provides the index of the outputword | 1.918264 | 1.880726 | 1.019959 |
needle = tuple(needle)
haystack = tuple(haystack)
solutions = []
#equality check
if needle == haystack:
return [(needle, 2)]
if allowpartial:
minl =1
else:
minl = len(needle)
for l in range(minl,min(len(needle), len(haystack))+1):
#print "LEFT-DEBU... | def calculate_overlap(haystack, needle, allowpartial=True) | Calculate the overlap between two sequences. Yields (overlap, placement) tuples (multiple because there may be multiple overlaps!). The former is the part of the sequence that overlaps, and the latter is -1 if the overlap is on the left side, 0 if it is a subset, 1 if it overlaps on the right side, 2 if its an identica... | 3.628165 | 3.38038 | 1.073301 |
for i,regexp in list(enumerate(regexps)):
if isstring(regexp):
regexps[i] = re.compile(regexp)
tokens = []
begin = 0
for i, c in enumerate(text):
if begin > i:
continue
elif i == begin:
m = False
for regexp in regexps:
... | def tokenize(text, regexps=TOKENIZERRULES) | Tokenizes a string and returns a list of tokens
:param text: The text to tokenise
:type text: string
:param regexps: Regular expressions to use as tokeniser rules in tokenisation (default=_pynlpl.textprocessors.TOKENIZERRULES_)
:type regexps: Tuple/list of regular expressions to use in tokenisation
... | 3.367037 | 3.65463 | 0.921307 |
begin = 0
for i, token in enumerate(tokens):
if is_end_of_sentence(tokens, i):
yield tokens[begin:i+1]
begin = i+1
if begin <= len(tokens)-1:
yield tokens[begin:] | def split_sentences(tokens) | Split sentences (based on tokenised data), returns sentences as a list of lists of tokens, each sentence is a list of tokens | 2.250202 | 2.464463 | 0.91306 |
if sys.version < '3':
if isinstance(s,unicode):
return unicodedata.normalize('NFKD', s).encode('ASCII', 'ignore')
else:
return unicodedata.normalize('NFKD', unicode(s,encoding)).encode('ASCII', 'ignore')
else:
if isinstance(s,bytes): s = str(s,encoding)
... | def strip_accents(s, encoding= 'utf-8') | Strip characters with diacritics and return a flat ascii representation | 2.175481 | 2.043353 | 1.064662 |
assert maxdist >= 2
tokens = list(tokens)
if maxdist > len(tokens):
maxdist = len(tokens)
l = len(tokens)
for i in range(0,l - 1):
for permutation in permutations(tokens[i:i+maxdist]):
if permutation != tuple(tokens[i:i+maxdist]):
newtokens = tokens[:... | def swap(tokens, maxdist=2) | Perform a swap operation on a sequence of tokens, exhaustively swapping all tokens up to the maximum specified distance. This is a subset of all permutations. | 2.659284 | 2.508583 | 1.060074 |
if isinstance(keyword,tuple) and isinstance(keyword,list):
l = len(keyword)
else:
keyword = (keyword,)
l = 1
n = l + contextsize*2
focuspos = contextsize + 1
for ngram in Windower(tokens,n,None,None):
if ngram[focuspos:focuspos+l] == keyword:
yield ng... | def find_keyword_in_context(tokens, keyword, contextsize=1) | Find a keyword in a particular sequence of tokens, and return the local context. Contextsize is the number of words to the left and right. The keyword may have multiple word, in which case it should to passed as a tuple or list | 4.206357 | 3.814266 | 1.102796 |
e = self.data[self.start]
self.start += 1
if self.start > 5 and self.start > len(self.data)//2:
self.data = self.data[self.start:]
self.start = 0
return e | def pop(self) | Retrieve the next element in line, this will remove it from the queue | 3.089326 | 2.879076 | 1.073027 |
f = self.f(item)
if callable(f):
score = f()
else:
score = f
if not self.duplicates:
for s, i in self.data:
if s == score and item == i:
#item is a duplicate, don't add it
return False
... | def append(self, item) | Adds an item to the priority queue (in the right place), returns True if successfull, False if the item was blocked (because of a bad score) | 3.064399 | 2.851216 | 1.074769 |
if self.minimize:
return self.data.pop(0)[1]
else:
return self.data.pop()[1] | def pop(self) | Retrieve the next element in line, this will remove it from the queue | 4.76139 | 4.386494 | 1.085466 |
if self.minimize:
return self.data[i][0]
else:
return self.data[(-1 * i) - 1][0] | def score(self, i) | Return the score for item x (cheap lookup), Item 0 is always the best item | 4.858691 | 4.349029 | 1.11719 |
if self.minimize:
self.data = self.data[:n]
else:
self.data = self.data[-1 * n:] | def prune(self, n) | prune all but the first (=best) n items | 4.535503 | 3.570599 | 1.270236 |
self.data = random.sample(self.data, n) | def randomprune(self,n) | prune down to n items at random, disregarding their score | 6.315843 | 4.429971 | 1.425707 |
if retainequalscore:
if self.minimize:
f = lambda x: x[0] <= score
else:
f = lambda x: x[0] >= score
else:
if self.minimize:
f = lambda x: x[0] < score
else:
f = lambda x: x[0] > scor... | def prunebyscore(self, score, retainequalscore=False) | Deletes all items below/above a certain score from the queue, depending on whether minimize is True or False. Note: It is recommended (more efficient) to use blockworse=True / blockequal=True instead! Preventing the addition of 'worse' items. | 1.951658 | 1.718258 | 1.135835 |
if not isinstance(item, Tree):
return ValueError("Can only append items of type Tree")
if not self.children: self.children = []
item.parent = self
self.children.append(item) | def append(self, item) | Add an item to the Tree | 3.773808 | 3.287379 | 1.147969 |
if self.children:
return sum( ( c.size() for c in self.children.values() ) ) + 1
else:
return 1 | def size(self) | Size is number of nodes under the trie, including the current node | 3.820153 | 3.063506 | 1.246987 |
if self.children:
if not maxdepth or (maxdepth and _depth < maxdepth):
for key, child in self.children.items():
if child.leaf():
yield child
else:
for results in child.walk(leavesonly, ma... | def walk(self, leavesonly=True, maxdepth=None, _depth = 0) | Depth-first search, walking through trie, returning all encounterd nodes (by default only leaves) | 2.485551 | 2.29437 | 1.083326 |
prevp = 0
prevs = 0
sentence = [];
sentence_id = ""
for word, id, pos, lemma in iter(self):
try:
doc_id, ptype, p, s, w = re.findall('([\w\d-]+)\.(p|head)\.(\d+)\.s\.(\d+)\.w\.(\d+)',id)[0]
if ((p != prevp) or (s != prevs)) and... | def sentences(self) | Iterate over all sentences (sentence_id, sentence) in the document, sentence is a list of 4-tuples (word,id,pos,lemma) | 2.918547 | 2.57253 | 1.134505 |
prevp = 0
partext = []
for word, id, pos, lemma in iter(self):
doc_id, ptype, p, s, w = re.findall('([\w\d-]+)\.(p|head)\.(\d+)\.s\.(\d+)\.w\.(\d+)',id)[0]
if prevp != p and partext:
yield ( doc_id + "." + ptype + "." + prevp , " ".join(partex... | def paragraphs(self, with_id = False) | Extracts paragraphs, returns list of plain-text(!) paragraphs | 4.553851 | 4.568027 | 0.996897 |
#TODO: download XSD from web
if self.inline:
xmlschema = ElementTree.XMLSchema(ElementTree.parse(StringIO("\n".join(open(formats_dir+"dcoi-dsc.xsd").readlines()))))
xmlschema.assertValid(self.tree)
#return xmlschema.validate(self)
else:
xm... | def validate(self, formats_dir="../formats/") | checks if the document is valid | 5.072318 | 4.844937 | 1.046932 |
global namespaces
return self.tree.xpath(expression, namespaces=namespaces) | def xpath(self, expression) | Executes an xpath expression using the correct namespaces | 8.032832 | 6.176901 | 1.300463 |
targetwords = []
for i, (word,lemma,postag) in enumerate(zip(datatuple[0],datatuple[1],datatuple[2])):
if word:
subwords = word.split("_")
for w in subwords: #split multiword expressions
targetwords.append( (w, lemma, postag, i, le... | def align(self, referencewords, datatuple) | align the reference sentence with the tagged data | 3.151972 | 3.120832 | 1.009978 |
if self.mainsetcache:
return self.mainsetcache
set_uri = self.get_set_uri()
for row in self.graph.query("SELECT ?seturi ?setid ?setlabel ?setopen ?setempty WHERE { ?seturi rdf:type skos:Collection . OPTIONAL { ?seturi skos:notation ?setid } OPTIONAL { ?seturi skos:prefLabel ... | def mainset(self) | Returns information regarding the set | 3.059313 | 3.016162 | 1.014307 |
if subset_id in self.subsetcache:
return self.subsetcache[subset_id]
set_uri = self.get_set_uri(subset_id)
for row in self.graph.query("SELECT ?seturi ?setid ?setlabel ?setopen WHERE { ?seturi rdf:type skos:Collection . OPTIONAL { ?seturi skos:notation ?setid } OPTIONAL { ?s... | def subset(self, subset_id) | Returns information regarding the set | 2.764326 | 2.658463 | 1.039821 |
classes = self.classes(set_uri_or_id, nestedhierarchy)
for classid in self.classorder(classes):
yield classes[classid] | def orderedclasses(self, set_uri_or_id=None, nestedhierarchy=False) | Higher-order generator function that yields class information in the right order, combines calls to :meth:`SetDefinition.classes` and :meth:`SetDefinition.classorder` | 3.808137 | 3.303462 | 1.152771 |
if set_uri_or_id and set_uri_or_id.startswith(('http://','https://')):
set_uri = set_uri_or_id
else:
set_uri = self.get_set_uri(set_uri_or_id)
assert set_uri is not None
classes= {}
uri2idmap = {}
for row in self.graph.query("SELECT ?cla... | def classes(self, set_uri_or_id=None, nestedhierarchy=False) | Returns a dictionary of classes for the specified (sub)set (if None, default, the main set is selected) | 2.240683 | 2.209358 | 1.014178 |
return [ classid for classid, classitem in sorted( ((classid, classitem) for classid, classitem in classes.items() if 'seqnr' in classitem) , key=lambda pair: pair[1]['seqnr'] )] + \
[ classid for classid, classitem in sorted( ((classid, classitem) for classid, classitem in classes.items... | def classorder(self,classes) | Return a list of class IDs in order for presentational purposes: order is determined first and foremost by explicit ordering, else alphabetically by label or as a last resort by class ID | 2.586968 | 2.322355 | 1.113942 |
self.lexer = ply.lex.lex(object=self, **kwargs) | def build(self, **kwargs) | Build the lexer. | 7.763836 | 3.624951 | 2.141777 |
if tree.tag == 'identifier':
return tree.attrib['name']
if tree.tag in ('string', 'boolean'):
return tree.text
if tree.tag == 'number':
return tree.attrib['value']
if tree.tag in ('property', 'object'):
return make_varname(_xpath_one(tree, '*'))
if tree.tag.e... | def make_varname(tree) | <left> tree </left> | 2.37267 | 2.384996 | 0.994832 |
auth_string = os.environ.get(env_prefix + 'WSGI_AUTH_CREDENTIALS')
if not auth_string:
return {}
result = {}
for credentials in auth_string.split('|'):
username, password = credentials.split(':', 1)
result[username] = password
return result | def _users_from_environ(env_prefix='') | Environment value via `user:password|user2:password2` | 2.826556 | 2.423023 | 1.166541 |
paths = os.environ.get(env_prefix + 'WSGI_AUTH_EXCLUDE_PATHS')
if not paths:
return []
return paths.split(';') | def _exclude_paths_from_environ(env_prefix='') | Environment value via `/login;/register` | 4.075587 | 3.329314 | 1.224152 |
paths = os.environ.get(env_prefix + 'WSGI_AUTH_PATHS')
if not paths:
return []
return paths.split(';') | def _include_paths_from_environ(env_prefix='') | Environment value via `/login;/register` | 4.870564 | 3.64868 | 1.334884 |
if self._is_request_in_include_path(request):
if self._is_request_in_exclude_path(request):
return True
else:
auth = request.authorization
if auth and auth[0] == 'Basic':
credentials = b64decode(auth[1]).decode(... | def is_authorized(self, request) | Check if the user is authenticated for the given request.
The include_paths and exclude_paths are first checked. If
authentication is required then the Authorization HTTP header is
checked against the credentials. | 2.511236 | 2.270371 | 1.106091 |
response = HTTPUnauthorized()
response.www_authenticate = ('Basic', {'realm': self._realm})
return response(environ, start_response) | def _login(self, environ, start_response) | Send a login response back to the client. | 4.958553 | 4.522533 | 1.096411 |
if self._include_paths:
for path in self._include_paths:
if request.path.startswith(path):
return True
return False
else:
return True | def _is_request_in_include_path(self, request) | Check if the request path is in the `_include_paths` list.
If no specific include paths are given then we assume that
authentication is required for all paths. | 2.327203 | 1.963186 | 1.185421 |
if self._exclude_paths:
for path in self._exclude_paths:
if request.path.startswith(path):
return True
return False
else:
return False | def _is_request_in_exclude_path(self, request) | Check if the request path is in the `_exclude_paths` list | 2.300144 | 1.800388 | 1.277583 |
prompt_kwargs = prompt_kwargs or {}
defaults = {
"history": InMemoryHistory(),
"completer": ClickCompleter(group),
"message": u"> ",
}
for key in defaults:
default_value = defaults[key]
if key not in prompt_kwargs:
prompt_kwargs[key] = default_v... | def bootstrap_prompt(prompt_kwargs, group) | Bootstrap prompt_toolkit kwargs or use user defined values.
:param prompt_kwargs: The user specified prompt kwargs. | 3.263362 | 3.729604 | 0.874989 |
# parent should be available, but we're not going to bother if not
group_ctx = old_ctx.parent or old_ctx
group = group_ctx.command
isatty = sys.stdin.isatty()
# Delete the REPL command from those available, as we don't want to allow
# nesting REPLs (note: pass `None` to `pop` as we don't w... | def repl( # noqa: C901
old_ctx,
prompt_kwargs=None,
allow_system_commands=True,
allow_internal_commands=True,
) | Start an interactive shell. All subcommands are available in it.
:param old_ctx: The current Click context.
:param prompt_kwargs: Parameters passed to
:py:func:`prompt_toolkit.shortcuts.prompt`.
If stdin is not a TTY, no prompt will be printed, but only commands read
from stdin. | 3.390891 | 3.410112 | 0.994363 |
group.command(name=name)(click.pass_context(repl)) | def register_repl(group, name="repl") | Register :func:`repl()` as sub-command *name* of *group*. | 9.57271 | 7.680469 | 1.246371 |
if command.startswith(":"):
target = _get_registered_target(command[1:], default=None)
if target:
return target() | def handle_internal_commands(command) | Run repl-internal commands.
Repl-internal commands are all commands starting with ":". | 7.274225 | 7.26974 | 1.000617 |
D = self._initialize(X)
for i in range(self.max_iter):
gamma = self._transform(D, X)
e = np.linalg.norm(X - gamma.dot(D))
if e < self.tol:
break
D, gamma = self._update_dict(X, D, gamma)
self.components_ = D
return... | def fit(self, X) | Parameters
----------
X: shape = [n_samples, n_features] | 3.544769 | 3.859171 | 0.918531 |
'''
Given a function to map from an ID to an underlying object, and a function
to map from an underlying object to the concrete GraphQLObjectType it
corresponds to, constructs a `Node` interface that objects can implement,
and a field config for a `node` root field.
If the type_resolver is omit... | def node_definitions(id_fetcher, type_resolver=None, id_resolver=None) | Given a function to map from an ID to an underlying object, and a function
to map from an underlying object to the concrete GraphQLObjectType it
corresponds to, constructs a `Node` interface that objects can implement,
and a field config for a `node` root field.
If the type_resolver is omitted, object ... | 3.925619 | 1.697994 | 2.311916 |
'''
Takes the "global ID" created by toGlobalID, and retuns the type name and ID
used to create it.
'''
unbased_global_id = unbase64(global_id)
_type, _id = unbased_global_id.split(':', 1)
return _type, _id | def from_global_id(global_id) | Takes the "global ID" created by toGlobalID, and retuns the type name and ID
used to create it. | 6.228088 | 2.547439 | 2.444843 |
'''
Creates the configuration for an id field on a node, using `to_global_id` to
construct the ID from the provided typename. The type-specific ID is fetcher
by calling id_fetcher on the object, or if not provided, by accessing the `id`
property on the object.
'''
return GraphQLField(
... | def global_id_field(type_name, id_fetcher=None) | Creates the configuration for an id field on a node, using `to_global_id` to
construct the ID from the provided typename. The type-specific ID is fetcher
by calling id_fetcher on the object, or if not provided, by accessing the `id`
property on the object. | 4.841914 | 1.954889 | 2.476823 |
'''
A simple function that accepts an array and connection arguments, and returns
a connection object for use in GraphQL. It uses array offsets as pagination,
so pagination will only work if the array is static.
'''
_len = len(data)
return connection_from_list_slice(
data,
ar... | def connection_from_list(data, args=None, **kwargs) | A simple function that accepts an array and connection arguments, and returns
a connection object for use in GraphQL. It uses array offsets as pagination,
so pagination will only work if the array is static. | 6.283294 | 2.41208 | 2.604928 |
'''
A version of `connectionFromArray` that takes a promised array, and returns a
promised connection.
'''
return data_promise.then(lambda data: connection_from_list(data, args, **kwargs)) | def connection_from_promised_list(data_promise, args=None, **kwargs) | A version of `connectionFromArray` that takes a promised array, and returns a
promised connection. | 5.727461 | 3.1263 | 1.832025 |
'''
Given a slice (subset) of an array, returns a connection object for use in
GraphQL.
This function is similar to `connectionFromArray`, but is intended for use
cases where you know the cardinality of the connection, consider it too large
to materialize the entire array, and instead wish pass ... | def connection_from_list_slice(list_slice, args=None, connection_type=None,
edge_type=None, pageinfo_type=None,
slice_start=0, list_length=0, list_slice_length=None) | Given a slice (subset) of an array, returns a connection object for use in
GraphQL.
This function is similar to `connectionFromArray`, but is intended for use
cases where you know the cardinality of the connection, consider it too large
to materialize the entire array, and instead wish pass in a slice o... | 2.433667 | 1.763791 | 1.379794 |
'''
Return the cursor associated with an object in an array.
'''
if _object not in data:
return None
offset = data.index(_object)
return offset_to_cursor(offset) | def cursor_for_object_in_connection(data, _object) | Return the cursor associated with an object in an array. | 5.384243 | 3.68172 | 1.462426 |
'''
Given an optional cursor and a default offset, returns the offset
to use; if the cursor contains a valid offset, that will be used,
otherwise it will be the default.
'''
if not is_str(cursor):
return default_offset
offset = cursor_to_offset(cursor)
try:
return int(of... | def get_offset_with_default(cursor=None, default_offset=0) | Given an optional cursor and a default offset, returns the offset
to use; if the cursor contains a valid offset, that will be used,
otherwise it will be the default. | 3.98127 | 2.254083 | 1.766248 |
edges = [{'source': s, 'target': t} for s, t in data]
nodes = force_directed_layout.run(edges, iterations, force_strength,
dampening, max_velocity, max_distance,
is_3d)
return {'edges': edges, 'nodes': nodes} | def generate(data, iterations=1000, force_strength=5.0, dampening=0.01,
max_velocity=2.0, max_distance=50, is_3d=True) | Runs a force-directed algorithm on a graph, returning a data structure.
Args:
data: An adjacency list of tuples (ie. [(1,2),...])
iterations: (Optional) Number of FDL iterations to run in coordinate
generation
force_strength: (Optional) Strength of Coulomb and Hooke forces
... | 2.898435 | 2.881119 | 1.00601 |
return json.dumps(obj, sort_keys=True, separators=(',', ':'),
cls=CustomEncoder) | def compress(obj) | Outputs json without whitespace. | 3.540116 | 2.901616 | 1.22005 |
return json.dumps(obj, indent=4, sort_keys=True, cls=CustomEncoder) | def dumps(obj) | Outputs json with formatting edits + object handling. | 3.234043 | 2.917868 | 1.108358 |
s = super(CustomEncoder, self).encode(obj)
# If uncompressed, postprocess for formatting
if len(s.splitlines()) > 1:
s = self.postprocess(s)
return s | def encode(self, obj) | Fired for every object. | 6.178361 | 6.042747 | 1.022443 |
is_compressing, is_hash, compressed, spaces = False, False, [], 0
for row in json_string.split('\n'):
if is_compressing:
if (row[:spaces + 5] == ' ' * (spaces + 4) +
('"' if is_hash else '{')):
compressed.append(row.rstrip(... | def postprocess(self, json_string) | Displays each entry on its own line. | 4.149051 | 3.930341 | 1.055646 |
# Get a list of node ids from the edge data
nodes = set(e['source'] for e in edges) | set(e['target'] for e in edges)
# Convert to a data-storing object and initialize some values
d = 3 if is_3d else 2
nodes = {n: {'velocity': [0.0] * d, 'force': [0.0] * d} for n in nodes}
# Repeat n tim... | def run(edges, iterations=1000, force_strength=5.0, dampening=0.01,
max_velocity=2.0, max_distance=50, is_3d=True) | Runs a force-directed-layout algorithm on the input graph.
iterations - Number of FDL iterations to run in coordinate generation
force_strength - Strength of Coulomb and Hooke forces
(edit this to scale the distance between nodes)
dampening - Multiplier to reduce force applied to nodes... | 3.911408 | 3.815891 | 1.025032 |
# Get relevant positional data
delta = [x2 - x1 for x1, x2 in zip(n1['velocity'], n2['velocity'])]
distance = sqrt(sum(d ** 2 for d in delta))
# If the deltas are too small, use random values to keep things moving
if distance < 0.1:
delta = [uniform(0.1, 0.2) for _ in repeat(None, 3)]
... | def _coulomb(n1, n2, k, r) | Calculates Coulomb forces and updates node data. | 3.300904 | 3.084999 | 1.069985 |
logger.debug("started")
context.clear()
logger.info(f"Context wiped. New context size: {len(context)}")
logger.debug("done") | def run_step(context) | Wipe the entire context.
Args:
Context is a dictionary or dictionary-like.
Does not require any specific keys in context. | 7.736632 | 7.097061 | 1.090118 |
assert context_arg, ("pipeline must be invoked with context arg set. For "
"this json parser you're looking for something "
"like: "
"pypyr pipelinename './myjsonfile.json'")
logger.debug("starting")
# open the json file on disk... | def get_parsed_context(context_arg) | Parse input context string and returns context as dictionary. | 7.504802 | 7.484313 | 1.002737 |
logger.debug("started")
context.assert_key_has_value(key='pathCheck', caller=__name__)
paths_to_check = context['pathCheck']
if not paths_to_check:
raise KeyInContextHasNoValueError("context['pathCheck'] must have a "
f"value for {__name__}.")
... | def run_step(context) | pypyr step that checks if a file or directory path exists.
Args:
context: pypyr.context.Context. Mandatory.
The following context key must exist
- pathsToCheck. str/path-like or list of str/paths.
Path to file on disk to check.
All input... | 3.674255 | 2.722688 | 1.349496 |
logger.debug("started")
context.assert_child_key_has_value('fileWriteJson', 'path', __name__)
out_path = context.get_formatted_string(context['fileWriteJson']['path'])
# doing it like this to safeguard against accidentally dumping all context
# with potentially sensitive values in it to disk i... | def run_step(context) | Write payload out to json file.
Args:
context: pypyr.context.Context. Mandatory.
The following context keys expected:
- fileWriteJson
- path. mandatory. path-like. Write output file to
here. Will create directories in path for you.
... | 4.586438 | 3.717387 | 1.23378 |
logger.debug("started")
(pipeline_name,
use_parent_context,
pipe_arg,
skip_parse,
raise_error,
loader,
) = get_arguments(context)
try:
if use_parent_context:
logger.info(f"pyping {pipeline_name}, using parent context.")
pipelinerunner.load... | def run_step(context) | Run another pipeline from this step.
The parent pipeline is the current, executing pipeline. The invoked, or
child pipeline is the pipeline you are calling from this step.
Args:
context: dictionary-like pypyr.context.Context. context is mandatory.
Uses the following context keys i... | 4.030962 | 3.306196 | 1.219214 |
context.assert_key_has_value(key='pype', caller=__name__)
pype = context.get_formatted('pype')
try:
pipeline_name = pype['name']
if pipeline_name is None:
raise KeyInContextHasNoValueError(
"pypyr.steps.pype ['pype']['name'] exists but is empty.")
excep... | def get_arguments(context) | Parse arguments for pype from context and assign default values.
Args:
context: pypyr.context.Context. context is mandatory.
Returns:
tuple (pipeline_name, #str
use_parent_context, #bool
pipe_arg, #str
skip_parse, #bool
raise_error #b... | 3.854171 | 2.327638 | 1.655829 |
logger.debug("starting")
# look for name.yaml in the pipelines/ sub-directory
logger.debug(f"current directory is {working_directory}")
# looking for {cwd}/pipelines/[pipeline_name].yaml
pipeline_path = os.path.abspath(os.path.join(
working_directory,
'pipelines',
pipe... | def get_pipeline_path(pipeline_name, working_directory) | Look for the pipeline in the various places it could be.
First checks the cwd. Then checks pypyr/pipelines dir.
Args:
pipeline_name: string. Name of pipeline to find
working_directory: string. Path in which to look for pipeline_name.yaml
Returns:
Absolute path to the pipeline_name... | 2.47594 | 2.286536 | 1.082835 |
logger.debug("starting")
pipeline_path = get_pipeline_path(
pipeline_name=pipeline_name,
working_directory=working_dir)
logger.debug(f"Trying to open pipeline at path {pipeline_path}")
try:
with open(pipeline_path) as yaml_file:
pipeline_definition = pypyr.yaml... | def get_pipeline_definition(pipeline_name, working_dir) | Open and parse the pipeline definition yaml.
Parses pipeline yaml and returns dictionary representing the pipeline.
pipeline_name.yaml should be in the working_dir/pipelines/ directory.
Args:
pipeline_name: string. Name of pipeline. This will be the file-name of
the pipelin... | 3.545114 | 3.777203 | 0.938555 |
return representer.represent_scalar(cls.yaml_tag, node.value) | def to_yaml(cls, representer, node) | How to serialize this class back to yaml. | 3.442521 | 2.885491 | 1.193045 |
if self.value:
return expressions.eval_string(self.value, context)
else:
# Empty input raises cryptic EOF syntax err, this more human
# friendly
raise ValueError('!py string expression is empty. It must be a '
'valid p... | def get_value(self, context) | Run python eval on the input string. | 23.730183 | 17.44957 | 1.359929 |
logger.debug("starting")
# Loop decorators only evaluated once, not for every step repeat
# execution.
foreach = context.get_formatted_iterable(self.foreach_items)
foreach_length = len(foreach)
logger.info(f"foreach decorator will loop {foreach_length} times."... | def foreach_loop(self, context) | Run step once for each item in foreach_items.
On each iteration, the invoked step can use context['i'] to get the
current iterator value.
Args:
context: (pypyr.context.Context) The pypyr context. This arg will
mutate. | 8.789891 | 7.262051 | 1.210387 |
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