text_prompt stringlengths 157 13.1k | code_prompt stringlengths 7 19.8k ⌀ |
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def equivalent_vertices(self):
"""A dictionary with symmetrically equivalent vertices.""" |
level1 = {}
for i, row in enumerate(self.vertex_fingerprints):
key = row.tobytes()
l = level1.get(key)
if l is None:
l = set([i])
level1[key] = l
else:
l.add(i)
level2 = {}
for key, vertices ... |
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def symmetry_cycles(self):
"""The cycle representations of the graph symmetries""" |
result = set([])
for symmetry in self.symmetries:
result.add(symmetry.cycles)
return result |
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def canonical_order(self):
"""The vertices in a canonical or normalized order. This routine will return a list of vertices in an order that does not depend on th... |
# A) find an appropriate starting vertex.
# Here we take a central vertex that has a minimal number of symmetrical
# equivalents, 'the highest atom number', and the highest fingerprint.
# Note that the symmetrical equivalents are computed from the vertex
# fingerprints, i.e. wit... |
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def iter_breadth_first(self, start=None, do_paths=False, do_duplicates=False):
"""Iterate over the vertices with the breadth first algorithm. See http://en.wikip... |
if start is None:
start = self.central_vertex
else:
try:
start = int(start)
except ValueError:
raise TypeError("First argument (start) must be an integer.")
if start < 0 or start >= self.num_vertices:
raise ... |
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def iter_breadth_first_edges(self, start=None):
"""Iterate over the edges with the breadth first convention. We need this for the pattern matching algorithms, bu... |
if start is None:
start = self.central_vertex
else:
try:
start = int(start)
except ValueError:
raise TypeError("First argument (start) must be an integer.")
if start < 0 or start >= self.num_vertices:
raise ... |
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def get_subgraph(self, subvertices, normalize=False):
"""Constructs a subgraph of the current graph Arguments: | ``subvertices`` -- The vertices that should be r... |
if normalize:
revorder = dict((j, i) for i, j in enumerate(subvertices))
new_edges = []
old_edge_indexes = []
for counter, (i, j) in enumerate(self.edges):
new_i = revorder.get(i)
if new_i is None:
continue
... |
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def get_vertex_fingerprints(self, vertex_strings, edge_strings, num_iter=None):
"""Return an array with fingerprints for each vertex""" |
import hashlib
def str2array(x):
"""convert a hash string to a numpy array of bytes"""
if len(x) == 0:
return np.zeros(0, np.ubyte)
elif sys.version_info[0] == 2:
return np.frombuffer(x, np.ubyte)
else:
retu... |
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def get_part(self, vertex_in, vertices_border):
"""List all vertices that are connected to vertex_in, but are not included in or 'behind' vertices_border. """ |
vertices_new = set(self.neighbors[vertex_in])
vertices_part = set([vertex_in])
while len(vertices_new) > 0:
pivot = vertices_new.pop()
if pivot in vertices_border:
continue
vertices_part.add(pivot)
pivot_neighbors = set(self.neigh... |
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def full_match(self, other):
"""Find the mapping between vertex indexes in self and other. This also works on disconnected graphs. Derived classes should just im... |
# we need normalize subgraphs because these graphs are used as patterns.
graphs0 = [
self.get_subgraph(group, normalize=True)
for group in self.independent_vertices
]
graphs1 = [
other.get_subgraph(group)
for group in other.independent_ver... |
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def add_relation(self, source, destination):
"""Add new a relation to the bejection""" |
if self.in_sources(source):
if self.forward[source] != destination:
raise ValueError("Source is already in use. Destination does "
"not match.")
else:
raise ValueError("Source-Destination relation already exists.")
... |
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def add_relations(self, relations):
"""Add multiple relations to a bijection""" |
for source, destination in relations:
self.add_relation(source, destination) |
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def inverse(self):
"""Returns the inverse bijection.""" |
result = self.__class__()
result.forward = copy.copy(self.reverse)
result.reverse = copy.copy(self.forward)
return result |
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def from_first_relation(cls, vertex0, vertex1):
"""Intialize a fresh match based on the first relation""" |
result = cls([(vertex0, vertex1)])
result.previous_ends1 = set([vertex1])
return result |
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def get_new_edges(self, subject_graph):
"""Get new edges from the subject graph for the graph search algorithm The Graph search algorithm extends the matches ite... |
result = []
#print "Match.get_new_edges self.previous_ends1", self.previous_ends1
for vertex in self.previous_ends1:
for neighbor in subject_graph.neighbors[vertex]:
if neighbor not in self.reverse:
result.append((vertex, neighbor))
return... |
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def copy_with_new_relations(self, new_relations):
"""Create a new match object extended with new relations""" |
result = self.__class__(self.forward.items())
result.add_relations(new_relations.items())
result.previous_ends1 = set(new_relations.values())
return result |
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def _set_pattern_graph(self, pattern_graph):
"""Initialize the pattern_graph""" |
self.pattern_graph = pattern_graph
self.level_edges = {}
self.level_constraints = {}
self.duplicate_checks = set([])
if pattern_graph is None:
return
if len(pattern_graph.independent_vertices) != 1:
raise ValueError("A pattern_graph must not be a ... |
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def iter_final_matches(self, canonical_match, subject_graph, one_match):
"""Given a match, iterate over all related equivalent matches When criteria sets are def... |
if self.criteria_sets is None or one_match:
yield canonical_match
else:
for criteria_set in self.criteria_sets:
satisfied_match_tags = set([])
for symmetry in self.pattern_graph.symmetries:
final_match = canonical_match * symme... |
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def get_closed_cycles(self):
"""Return the closed cycles corresponding to this permutation The cycle will be normalized to facilitate the elimination of duplicat... |
# A) construct all the cycles
closed_cycles = []
todo = set(self.forward.keys())
if todo != set(self.forward.values()):
raise GraphError("The subject and pattern graph must have the same "
"numbering.")
current_vertex = None
while... |
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def compare(self, vertex0, vertex1, subject_graph):
"""Returns true when the two vertices are of the same kind""" |
return (
self.pattern_graph.vertex_fingerprints[vertex0] ==
subject_graph.vertex_fingerprints[vertex1]
).all() |
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def complete(self, match, subject_graph):
"""Check the completeness of a ring match""" |
size = len(match)
# check whether we have an odd strong ring
if match.forward[size-1] in subject_graph.neighbors[match.forward[size-2]]:
# we have an odd closed cycle. check if this is a strong ring
order = list(range(0, size, 2)) + list(range(1, size-1, 2))[::-1]
... |
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def print_debug(self, text, indent=0):
"""Only prints debug info on screen when self.debug == True.""" |
if self.debug:
if indent > 0:
print(" "*self.debug, text)
self.debug += indent
if indent <= 0:
print(" "*self.debug, text) |
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def _iter_candidate_groups(self, init_match, edges0, edges1):
"""Divide the edges into groups""" |
# collect all end vertices0 and end vertices1 that belong to the same
# group.
sources = {}
for start_vertex0, end_vertex0 in edges0:
l = sources.setdefault(start_vertex0, [])
l.append(end_vertex0)
dests = {}
for start_vertex1, end_vertex1 in edge... |
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def _iter_new_relations(self, init_match, subject_graph, edges0, constraints0, edges1):
"""Given an onset for a match, iterate over all possible new key-value pa... |
# Count the number of unique edges0[i][1] values. This is also
# the number of new relations.
num_new_relations = len(set(j for i, j in edges0))
def combine_small(relations, num):
"""iterate over all compatible combinations within one set of relations"""
if len(... |
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def _iter_matches(self, input_match, subject_graph, one_match, level=0):
"""Given an onset for a match, iterate over all completions of that match This iterator ... |
self.print_debug("ENTERING _ITER_MATCHES", 1)
self.print_debug("input_match: %s" % input_match)
# A) collect the new edges in the pattern graph and the subject graph
# to extend the match.
#
# Note that the edges are ordered. edge[0] is always in the match.
# edg... |
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def dump_pdb(filename, molecule, atomnames=None, resnames=None, chain_ids=None, occupancies=None, betas=None):
"""Writes a single molecule to a pdb file. This fu... |
with open(filename, "w") as f:
res_id = 1
old_resname = None
for i in range(molecule.size):
symbol = periodic[molecule.numbers[i]].symbol
if atomnames is None:
atomname = symbol
else:
atomname = atomnames[i]
i... |
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def load_pdb(filename):
"""Loads a single molecule from a pdb file. This function does support only a small fragment from the pdb specification. It assumes that ... |
with open(filename) as f:
numbers = []
coordinates = []
occupancies = []
betas = []
for line in f:
if line.startswith("ATOM"):
symbol = line[76:78].strip()
numbers.append(periodic[symbol].number)
coordinates.append(... |
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def zmat_to_cart(zmat):
"""Converts a ZMatrix back to cartesian coordinates.""" |
numbers = zmat["number"]
N = len(numbers)
coordinates = np.zeros((N, 3), float)
# special cases for the first coordinates
coordinates[1, 2] = zmat["distance"][1]
if zmat["rel1"][2] == 1:
sign = -1
else:
sign = 1
coordinates[2, 2] = zmat["distance"][2]*sign*np.cos(zmat[... |
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def _get_new_ref(self, existing_refs):
"""Get a new reference atom for a row in the ZMatrix The reference atoms should obey the following conditions: - They must... |
# ref0 is the atom whose position is defined by the current row in the
# zmatrix.
ref0 = existing_refs[0]
for ref in existing_refs:
# try to find a neighbor of the ref that can serve as the new ref
result = None
for n in sorted(self.graph.neighbors[re... |
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def cart_to_zmat(self, coordinates):
"""Convert cartesian coordinates to ZMatrix format Argument: coordinates -- Cartesian coordinates (numpy array Nx3) The coor... |
N = len(self.graph.numbers)
if coordinates.shape != (N, 3):
raise ValueError("The shape of the coordinates must be (%i, 3)" % N)
result = np.zeros(N, dtype=self.dtype)
for i in range(N):
ref0 = self.old_index[i]
rel1 = -1
rel2 = -1
... |
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def can_map_ipa_string(self, ipa_string):
""" Return ``True`` if the mapper can map all the IPA characters in the given IPA string. :param IPAString ipa_string: ... |
canonical = [(c.canonical_representation, ) for c in ipa_string]
split = split_using_dictionary(canonical, self, self.max_key_length, single_char_parsing=False)
for sub in split:
if not sub in self.ipa_canonical_representation_to_mapped_str:
return False
retu... |
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def map_ipa_string(self, ipa_string, ignore=False, return_as_list=False, return_can_map=False):
""" Convert the given IPAString to a string containing the corres... |
acc = []
can_map = True
canonical = [(c.canonical_representation, ) for c in ipa_string]
split = split_using_dictionary(canonical, self, self.max_key_length, single_char_parsing=False)
for sub in split:
try:
acc.append(self.ipa_canonical_representatio... |
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def map_unicode_string(self, unicode_string, ignore=False, single_char_parsing=False, return_as_list=False, return_can_map=False):
""" Convert the given Unicode ... |
if unicode_string is None:
return None
ipa_string = IPAString(unicode_string=unicode_string, ignore=ignore, single_char_parsing=single_char_parsing)
return self.map_ipa_string(
ipa_string=ipa_string,
ignore=ignore,
return_as_list=return_as_list,
... |
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def print_invalid_chars(invalid_chars, vargs):
""" Print Unicode characterss that are not IPA valid, if requested by the user. :param list invalid_chars: a list ... |
if len(invalid_chars) > 0:
if vargs["print_invalid"]:
print(u"".join(invalid_chars))
if vargs["unicode"]:
for u_char in sorted(set(invalid_chars)):
print(u"'%s'\t%s\t%s" % (u_char, hex(ord(u_char)), unicodedata.name(u_char, "UNKNOWN"))) |
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def command_canonize(string, vargs):
""" Print the canonical representation of the given string. It will replace non-canonical compound characters with their can... |
try:
ipa_string = IPAString(
unicode_string=string,
ignore=vargs["ignore"],
single_char_parsing=vargs["single_char_parsing"]
)
print(vargs["separator"].join([(u"%s" % c) for c in ipa_string]))
except ValueError as exc:
print_error(str(exc)) |
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def command_chars(string, vargs):
""" Print a list of all IPA characters in the given string. It will print the Unicode representation, the full IPA name, and th... |
try:
ipa_string = IPAString(
unicode_string=string,
ignore=vargs["ignore"],
single_char_parsing=vargs["single_char_parsing"]
)
for c in ipa_string:
print(u"'%s'\t%s (%s)" % (c.unicode_repr, c.name, unicode_to_hex(c.unicode_repr)))
except V... |
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def command_check(string, vargs):
""" Check if the given string is IPA valid. If the given string is not IPA valid, print the invalid characters. :param str stri... |
is_valid = is_valid_ipa(string)
print(is_valid)
if not is_valid:
valid_chars, invalid_chars = remove_invalid_ipa_characters(
unicode_string=string,
return_invalid=True
)
print_invalid_chars(invalid_chars, vargs) |
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def command_clean(string, vargs):
""" Remove characters that are not IPA valid from the given string, and print the remaining string. :param str string: the stri... |
valid_chars, invalid_chars = remove_invalid_ipa_characters(
unicode_string=string,
return_invalid=True,
single_char_parsing=vargs["single_char_parsing"]
)
print(u"".join(valid_chars))
print_invalid_chars(invalid_chars, vargs) |
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def command_u2a(string, vargs):
""" Print the ARPABEY ASCII string corresponding to the given Unicode IPA string. :param str string: the string to act upon :para... |
try:
l = ARPABETMapper().map_unicode_string(
unicode_string=string,
ignore=vargs["ignore"],
single_char_parsing=vargs["single_char_parsing"],
return_as_list=True
)
print(vargs["separator"].join(l))
except ValueError as exc:
print_e... |
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def command_u2k(string, vargs):
""" Print the Kirshenbaum ASCII string corresponding to the given Unicode IPA string. :param str string: the string to act upon :... |
try:
l = KirshenbaumMapper().map_unicode_string(
unicode_string=string,
ignore=vargs["ignore"],
single_char_parsing=vargs["single_char_parsing"],
return_as_list=True
)
print(vargs["separator"].join(l))
except ValueError as exc:
pri... |
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def ipa_chars(self, value):
""" Set the list of IPAChar objects composing the IPA string :param list value: list of IPAChar objects """ |
if value is None:
self.__ipa_chars = []
else:
if is_list_of_ipachars(value):
self.__ipa_chars = value
else:
raise TypeError("ipa_chars only accepts a list of IPAChar objects") |
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def is_equivalent(self, other, ignore=False):
""" Return ``True`` if the IPA string is equivalent to the ``other`` object. The ``other`` object can be: 1. a Unic... |
def is_equivalent_to_list_of_ipachars(other):
"""
Return ``True`` if the list of IPAChar objects
in the canonical representation of the string
is the same as the given list.
:param list other: list of IPAChar objects
:rtype: bool
... |
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def filter_chars(self, chars=u""):
""" Return a new IPAString, containing only the IPA characters specified by the ``chars`` string. Valid values for ``chars`` a... |
if chars in [u"cns", u"consonants"]:
return self.consonants
elif chars in [u"vwl", u"vowels"]:
return self.vowels
elif chars in [u"cns_vwl", u"letters"]:
return self.letters
elif chars in [u"cns_vwl_pstr", u"cvp"]:
return self.cns_vwl_pstr... |
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def consonants(self):
""" Return a new IPAString, containing only the consonants in the current string. :rtype: IPAString """ |
return IPAString(ipa_chars=[c for c in self.ipa_chars if c.is_consonant]) |
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def vowels(self):
""" Return a new IPAString, containing only the vowels in the current string. :rtype: IPAString """ |
return IPAString(ipa_chars=[c for c in self.ipa_chars if c.is_vowel]) |
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def convert_unicode_field(string):
""" Convert a Unicode field into the corresponding list of Unicode strings. The (input) Unicode field is a Unicode string cont... |
values = []
for codepoint in [s for s in string.split(DATA_FILE_CODEPOINT_SEPARATOR) if (s != DATA_FILE_VALUE_NOT_AVAILABLE) and (len(s) > 0)]:
values.append(u"".join([hex_to_unichr(c) for c in codepoint.split(DATA_FILE_CODEPOINT_JOINER)]))
return values |
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def convert_ascii_field(string):
""" Convert an ASCII field into the corresponding list of Unicode strings. The (input) ASCII field is a Unicode string containin... |
values = []
for codepoint in [s for s in string.split(DATA_FILE_CODEPOINT_SEPARATOR) if (s != DATA_FILE_VALUE_NOT_AVAILABLE) and (len(s) > 0)]:
#if DATA_FILE_CODEPOINT_JOINER in codepoint:
# values.append(u"".join([hex_to_unichr(c) for c in codepoint.split(DATA_FILE_CODEPOINT_JOINER)]))
... |
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def convert_raw_tuple(value_tuple, format_string):
""" Convert a tuple of raw values, according to the given line format. :param tuple value_tuple: the tuple of ... |
values = []
for v, c in zip(value_tuple, format_string):
if v is None:
# append None
values.append(v)
elif c == u"s":
# string
values.append(v)
elif c == u"S":
# string, split using space as delimiter
values.append... |
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def load_data_file( file_path, file_path_is_relative=False, comment_string=DATA_FILE_COMMENT, field_separator=DATA_FILE_FIELD_SEPARATOR, line_format=None ):
""" ... |
raw_tuples = []
if file_path_is_relative:
file_path = os.path.join(os.path.dirname(__file__), file_path)
with io.open(file_path, "r", encoding="utf-8") as f:
for line in f:
line = line.strip()
if (len(line) > 0) and (not line.startswith(comment_string)):
... |
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def invalid_ipa_characters(unicode_string, indices=False):
""" Return the list of Unicode characters in the given Unicode string that are not IPA valid. Return `... |
if unicode_string is None:
return None
if indices:
return [(i, unicode_string[i]) for i in range(len(unicode_string)) if unicode_string[i] not in UNICODE_TO_IPA]
return set([c for c in unicode_string if c not in UNICODE_TO_IPA]) |
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def variant_to_list(obj):
""" Return a list containing the descriptors in the given object. The ``obj`` can be a list or a set of descriptor strings, or a Unicod... |
if isinstance(obj, list):
return obj
elif is_unicode_string(obj):
return [s for s in obj.split() if len(s) > 0]
elif isinstance(obj, set) or isinstance(obj, frozenset):
return list(obj)
raise TypeError("The given value must be a list or a set of descriptor strings, or a Unicode ... |
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def variant_to_canonical_string(obj):
""" Return a list containing the canonical string for the given object. The ``obj`` can be a list or a set of descriptor st... |
acc = [DG_ALL_DESCRIPTORS.canonical_value(p) for p in variant_to_list(obj)]
acc = sorted([a for a in acc if a is not None])
return u" ".join(acc) |
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def is_list_of_ipachars(obj):
""" Return ``True`` if the given object is a list of IPAChar objects. :param object obj: the object to test :rtype: bool """ |
if isinstance(obj, list):
for e in obj:
if not isinstance(e, IPAChar):
return False
return True
return False |
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def is_equivalent(self, other):
""" Return ``True`` if the IPA character is equivalent to the ``other`` object. The ``other`` object can be: 1. a Unicode string,... |
if (self.unicode_repr is not None) and (is_unicode_string(other)) and (self.unicode_repr == other):
return True
if isinstance(other, IPAChar):
return self.canonical_representation == other.canonical_representation
try:
return self.canonical_representation == ... |
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def dg_value(self, descriptor_group):
""" Return the canonical value of a descriptor of the character, provided it is present in the given descriptor group. If n... |
for p in self.descriptors:
if p in descriptor_group:
return descriptor_group.canonical_value(p)
return None |
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def has_descriptor(self, descriptor):
""" Return ``True`` if the character has the given descriptor. :param IPADescriptor descriptor: the descriptor to be checke... |
for p in self.descriptors:
if p in descriptor:
return True
return False |
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def voicing(self, value):
""" Set the voicing of the consonant. :param str value: the value to be set """ |
if (value is not None) and (not value in DG_C_VOICING):
raise ValueError("Unrecognized value for voicing: '%s'" % value)
self.__voicing = value |
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def place(self, value):
""" Set the place of articulation of the consonant. :param str value: the value to be set """ |
if (value is not None) and (not value in DG_C_PLACE):
raise ValueError("Unrecognized value for place: '%s'" % value)
self.__place = value |
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def manner(self, value):
""" Set the manner of articulation of the consonant. :param str value: the value to be set """ |
if (value is not None) and (not value in DG_C_MANNER):
raise ValueError("Unrecognized value for manner: '%s'" % value)
self.__manner = value |
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def height(self, value):
""" Set the height of the vowel. :param str value: the value to be set """ |
if (value is not None) and (not value in DG_V_HEIGHT):
raise ValueError("Unrecognized value for height: '%s'" % value)
self.__height = value |
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def backness(self, value):
""" Set the backness of the vowel. :param str value: the value to be set """ |
if (value is not None) and (not value in DG_V_BACKNESS):
raise ValueError("Unrecognized value for backness: '%s'" % value)
self.__backness = value |
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def roundness(self, value):
""" Set the roundness of the vowel. :param str value: the value to be set """ |
if (value is not None) and (not value in DG_V_ROUNDNESS):
raise ValueError("Unrecognized value for roundness: '%s'" % value)
self.__roundness = value |
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def _load_data(self):
""" Load the Kirshenbaum ASCII IPA data from the built-in database. """ |
ipa_canonical_string_to_ascii_str = dict()
for line in load_data_file(
file_path=self.DATA_FILE_PATH,
file_path_is_relative=True,
line_format=u"sxA"
):
i_desc, i_ascii = line
if len(i_ascii) == 0:
raise ValueError("Data... |
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def canonical_value(self, query):
""" Return the canonical value corresponding to the given query value. Return ``None`` if the query value is not present in any... |
for d in self.descriptors:
if query in d:
return d.canonical_label
return None |
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def _load_data(self):
""" Load the ARPABET ASCII IPA data from the built-in database. """ |
ipa_canonical_string_to_ascii_str = dict()
for line in load_data_file(
file_path=self.DATA_FILE_PATH,
file_path_is_relative=True,
line_format=u"UA"
):
i_unicode, i_ascii = line
if (len(i_unicode) == 0) or (len(i_ascii) == 0):
... |
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def is_unicode_string(string):
""" Return ``True`` if the given string is a Unicode string, that is, of type ``unicode`` in Python 2 or ``str`` in Python 3. Retu... |
if string is None:
return None
if PY2:
return isinstance(string, unicode)
return isinstance(string, str) |
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def to_unicode_string(string):
""" Return a Unicode string out of the given string. On Python 2, it calls ``unicode`` with ``utf-8`` encoding. On Python 3, it ju... |
if string is None:
return None
if is_unicode_string(string):
return string
# if reached here, string is a byte string
if PY2:
return unicode(string, encoding="utf-8")
return string.decode(encoding="utf-8") |
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def hex_to_unichr(hex_string):
""" Return the Unicode character with the given codepoint, given as an hexadecimal string. Return ``None`` if ``hex_string`` is ``... |
if (hex_string is None) or (len(hex_string) < 1):
return None
if hex_string.startswith("U+"):
hex_string = hex_string[2:]
return int_to_unichr(int(hex_string, base=16)) |
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def unicode_to_hex(unicode_string):
""" Return a string containing the Unicode hexadecimal codepoint of each Unicode character in the given Unicode string. Retur... |
if unicode_string is None:
return None
acc = []
for c in unicode_string:
s = hex(ord(c)).replace("0x", "").upper()
acc.append("U+" + ("0" * (4 - len(s))) + s)
return u" ".join(acc) |
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def etree_to_text(tree, guess_punct_space=True, guess_layout=True, newline_tags=NEWLINE_TAGS, double_newline_tags=DOUBLE_NEWLINE_TAGS):
""" Convert a html tree t... |
chunks = []
_NEWLINE = object()
_DOUBLE_NEWLINE = object()
class Context:
""" workaround for missing `nonlocal` in Python 2 """
# _NEWLINE, _DOUBLE_NEWLINE or content of the previous chunk (str)
prev = _DOUBLE_NEWLINE
def should_add_space(text, prev):
""" Return T... |
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def selector_to_text(sel, guess_punct_space=True, guess_layout=True):
""" Convert a cleaned parsel.Selector to text. See html_text.extract_text docstring for des... |
import parsel
if isinstance(sel, parsel.SelectorList):
# if selecting a specific xpath
text = []
for s in sel:
extracted = etree_to_text(
s.root,
guess_punct_space=guess_punct_space,
guess_layout=guess_layout)
if ex... |
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def cleaned_selector(html):
""" Clean parsel.selector. """ |
import parsel
try:
tree = _cleaned_html_tree(html)
sel = parsel.Selector(root=tree, type='html')
except (lxml.etree.XMLSyntaxError,
lxml.etree.ParseError,
lxml.etree.ParserError,
UnicodeEncodeError):
# likely plain text
sel = parsel.Select... |
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def extract_text(html, guess_punct_space=True, guess_layout=True, newline_tags=NEWLINE_TAGS, double_newline_tags=DOUBLE_NEWLINE_TAGS):
""" Convert html to text, ... |
if html is None:
return ''
cleaned = _cleaned_html_tree(html)
return etree_to_text(
cleaned,
guess_punct_space=guess_punct_space,
guess_layout=guess_layout,
newline_tags=newline_tags,
double_newline_tags=double_newline_tags,
) |
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def get_json(self, layer, where="1 = 1", fields=[], count_only=False, srid='4326'):
""" Gets the JSON file from ArcGIS """ |
params = {
'where': where,
'outFields': ", ".join(fields),
'returnGeometry': True,
'outSR': srid,
'f': "pjson",
'orderByFields': self.object_id_field,
'returnCountOnly': count_only
}
... |
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def get_descriptor_for_layer(self, layer):
""" Returns the standard JSON descriptor for the layer. There is a lot of usefule information in there. """ |
if not layer in self._layer_descriptor_cache:
params = {'f': 'pjson'}
if self.token:
params['token'] = self.token
response = requests.get(self._build_request(layer), params=params)
self._layer_descriptor_cache[layer] = response.json()
retu... |
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def enumerate_layer_fields(self, layer):
""" Pulls out all of the field names for a layer. """ |
descriptor = self.get_descriptor_for_layer(layer)
return [field['name'] for field in descriptor['fields']] |
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def get(self, layer, where="1 = 1", fields=[], count_only=False, srid='4326'):
""" Gets a layer and returns it as honest to God GeoJSON. WHERE 1 = 1 causes us to... |
base_where = where
# By default we grab all of the fields. Technically I think
# we can just do "*" for all fields, but I found this was buggy in
# the KMZ mode. I'd rather be explicit.
fields = fields or self.enumerate_layer_fields(layer)
jsobj = self.get_json(layer, w... |
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def getMultiple(self, layers, where="1 = 1", fields=[], srid='4326', layer_name_field=None):
""" Get a bunch of layers and concatenate them together into one. Th... |
features = []
for layer in layers:
get_fields = fields or self.enumerate_layer_fields(layer)
this_layer = self.get(layer, where, get_fields, False, srid).get('features')
if layer_name_field:
descriptor = self.get_descriptor_for_layer(layer)
... |
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| def get_version(extension, workflow_file):
'''Determines the version of a .py, .wdl, or .cwl file.'''
if extension == 'py' and two_seven_compatible(workflow_file):
return '2.7'
elif extension == 'cwl':
return yaml.load(open(workflow_file))['cwlVersion']
else: # Must be a wdl file.
... |
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def wf_info(workflow_path):
""" Returns the version of the file and the file extension. Assumes that the file path is to the file directly ie, ends with a valid ... |
supported_formats = ['py', 'wdl', 'cwl']
file_type = workflow_path.lower().split('.')[-1] # Grab the file extension
workflow_path = workflow_path if ':' in workflow_path else 'file://' + workflow_path
if file_type in supported_formats:
if workflow_path.startswith('file://'):
vers... |
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def run(self, wf, jsonyaml, attachments):
""" Composes and sends a post request that signals the wes server to run a workflow. :param str workflow_file: A local/... |
attachments = list(expand_globs(attachments))
parts = build_wes_request(wf, jsonyaml, attachments)
postresult = requests.post("%s://%s/ga4gh/wes/v1/runs" % (self.proto, self.host),
files=parts,
headers=self.auth)
retu... |
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def cancel(self, run_id):
""" Cancel a running workflow. :param run_id: String (typically a uuid) identifying the run. :param str auth: String to send in the aut... |
postresult = requests.post("%s://%s/ga4gh/wes/v1/runs/%s/cancel" % (self.proto, self.host, run_id),
headers=self.auth)
return wes_reponse(postresult) |
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def get_run_log(self, run_id):
""" Get detailed info about a running workflow. :param run_id: String (typically a uuid) identifying the run. :param str auth: Str... |
postresult = requests.get("%s://%s/ga4gh/wes/v1/runs/%s" % (self.proto, self.host, run_id),
headers=self.auth)
return wes_reponse(postresult) |
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def getstate(self):
""" Returns RUNNING, -1 COMPLETE, 0 or EXECUTOR_ERROR, 255 """ |
state = "RUNNING"
exit_code = -1
exitcode_file = os.path.join(self.workdir, "exit_code")
pid_file = os.path.join(self.workdir, "pid")
if os.path.exists(exitcode_file):
with open(exitcode_file) as f:
exit_code = int(f.read())
elif os.path.exi... |
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def write_workflow(self, request, opts, cwd, wftype='cwl'):
"""Writes a cwl, wdl, or python file as appropriate from the request dictionary.""" |
workflow_url = request.get("workflow_url")
# link the cwl and json into the cwd
if workflow_url.startswith('file://'):
os.link(workflow_url[7:], os.path.join(cwd, "wes_workflow." + wftype))
workflow_url = os.path.join(cwd, "wes_workflow." + wftype)
os.link(self... |
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def call_cmd(self, cmd, cwd):
""" Calls a command with Popen. Writes stdout, stderr, and the command to separate files. :param cmd: A string or array of strings.... |
with open(self.cmdfile, 'w') as f:
f.write(str(cmd))
stdout = open(self.outfile, 'w')
stderr = open(self.errfile, 'w')
logging.info('Calling: ' + ' '.join(cmd))
process = subprocess.Popen(cmd,
stdout=stdout,
... |
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def getstate(self):
""" Returns QUEUED, -1 INITIALIZING, -1 RUNNING, -1 COMPLETE, 0 or EXECUTOR_ERROR, 255 """ |
# the jobstore never existed
if not os.path.exists(self.jobstorefile):
logging.info('Workflow ' + self.run_id + ': QUEUED')
return "QUEUED", -1
# completed earlier
if os.path.exists(self.statcompletefile):
logging.info('Workflow ' + self.run_id + ': ... |
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def getopt(self, p, default=None):
"""Returns the first option value stored that matches p or default.""" |
for k, v in self.pairs:
if k == p:
return v
return default |
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def getoptlist(self, p):
"""Returns all option values stored that match p as a list.""" |
optlist = []
for k, v in self.pairs:
if k == p:
optlist.append(v)
return optlist |
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def catch_exceptions(orig_func):
"""Catch uncaught exceptions and turn them into http errors""" |
@functools.wraps(orig_func)
def catch_exceptions_wrapper(self, *args, **kwargs):
try:
return orig_func(self, *args, **kwargs)
except arvados.errors.ApiError as e:
logging.exception("Failure")
return {"msg": e._get_reason(), "status_code": e.resp.status}, int... |
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def _safe_name(file_name, sep):
"""Convert the file name to ASCII and normalize the string.""" |
file_name = stringify(file_name)
if file_name is None:
return
file_name = ascii_text(file_name)
file_name = category_replace(file_name, UNICODE_CATEGORIES)
file_name = collapse_spaces(file_name)
if file_name is None or not len(file_name):
return
return file_name.replace(WS, ... |
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def safe_filename(file_name, sep='_', default=None, extension=None):
"""Create a secure filename for plain file system storage.""" |
if file_name is None:
return decode_path(default)
file_name = decode_path(file_name)
file_name = os.path.basename(file_name)
file_name, _extension = os.path.splitext(file_name)
file_name = _safe_name(file_name, sep=sep)
if file_name is None:
return decode_path(default)
file... |
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def stringify(value, encoding_default='utf-8', encoding=None):
"""Brute-force convert a given object to a string. This will attempt an increasingly mean set of c... |
if value is None:
return None
if not isinstance(value, six.text_type):
if isinstance(value, (date, datetime)):
return value.isoformat()
elif isinstance(value, (float, Decimal)):
return Decimal(value).to_eng_string()
elif isinstance(value, six.binary_type... |
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def normalize_result(result, default, threshold=0.2):
"""Interpret a chardet result.""" |
if result is None:
return default
if result.get('confidence') is None:
return default
if result.get('confidence') < threshold:
return default
return normalize_encoding(result.get('encoding'),
default=default) |
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def guess_encoding(text, default=DEFAULT_ENCODING):
"""Guess string encoding. Given a piece of text, apply character encoding detection to guess the appropriate ... |
result = chardet.detect(text)
return normalize_result(result, default=default) |
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def guess_file_encoding(fh, default=DEFAULT_ENCODING):
"""Guess encoding from a file handle.""" |
start = fh.tell()
detector = chardet.UniversalDetector()
while True:
data = fh.read(1024 * 10)
if not data:
detector.close()
break
detector.feed(data)
if detector.done:
break
fh.seek(start)
return normalize_result(detector.result,... |
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def guess_path_encoding(file_path, default=DEFAULT_ENCODING):
"""Wrapper to open that damn file for you, lazy bastard.""" |
with io.open(file_path, 'rb') as fh:
return guess_file_encoding(fh, default=default) |
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def decompose_nfkd(text):
"""Perform unicode compatibility decomposition. This will replace some non-standard value representations in unicode and normalise them... |
if text is None:
return None
if not hasattr(decompose_nfkd, '_tr'):
decompose_nfkd._tr = Transliterator.createInstance('Any-NFKD')
return decompose_nfkd._tr.transliterate(text) |
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Description:
def compose_nfc(text):
"""Perform unicode composition.""" |
if text is None:
return None
if not hasattr(compose_nfc, '_tr'):
compose_nfc._tr = Transliterator.createInstance('Any-NFC')
return compose_nfc._tr.transliterate(text) |
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Solve the following problem using Python, implementing the functions described below, one line at a time
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Description:
def category_replace(text, replacements=UNICODE_CATEGORIES):
"""Remove characters from a string based on unicode classes. This is a method for removing non-text ... |
if text is None:
return None
characters = []
for character in decompose_nfkd(text):
cat = category(character)
replacement = replacements.get(cat, character)
if replacement is not None:
characters.append(replacement)
return u''.join(characters) |
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Solve the following problem using Python, implementing the functions described below, one line at a time
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Description:
def remove_unsafe_chars(text):
"""Remove unsafe unicode characters from a piece of text.""" |
if isinstance(text, six.string_types):
text = UNSAFE_RE.sub('', text)
return text |
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