repo
stringlengths
7
55
path
stringlengths
4
127
func_name
stringlengths
1
88
original_string
stringlengths
75
19.8k
language
stringclasses
1 value
code
stringlengths
75
19.8k
code_tokens
sequence
docstring
stringlengths
3
17.3k
docstring_tokens
sequence
sha
stringlengths
40
40
url
stringlengths
87
242
partition
stringclasses
1 value
christophertbrown/bioscripts
ctbBio/nr_fasta.py
append_index_id
def append_index_id(id, ids): """ add index to id to make it unique wrt ids """ index = 1 mod = '%s_%s' % (id, index) while mod in ids: index += 1 mod = '%s_%s' % (id, index) ids.append(mod) return mod, ids
python
def append_index_id(id, ids): """ add index to id to make it unique wrt ids """ index = 1 mod = '%s_%s' % (id, index) while mod in ids: index += 1 mod = '%s_%s' % (id, index) ids.append(mod) return mod, ids
[ "def", "append_index_id", "(", "id", ",", "ids", ")", ":", "index", "=", "1", "mod", "=", "'%s_%s'", "%", "(", "id", ",", "index", ")", "while", "mod", "in", "ids", ":", "index", "+=", "1", "mod", "=", "'%s_%s'", "%", "(", "id", ",", "index", ")", "ids", ".", "append", "(", "mod", ")", "return", "mod", ",", "ids" ]
add index to id to make it unique wrt ids
[ "add", "index", "to", "id", "to", "make", "it", "unique", "wrt", "ids" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/nr_fasta.py#L11-L21
train
christophertbrown/bioscripts
ctbBio/nr_fasta.py
de_rep
def de_rep(fastas, append_index, return_original = False): """ de-replicate fastas based on sequence names """ ids = [] for fasta in fastas: for seq in parse_fasta(fasta): header = seq[0].split('>')[1].split() id = header[0] if id not in ids: ids.append(id) if return_original is True: yield [header, seq] else: yield seq elif append_index == True: new, ids = append_index_id(id, ids) if return_original is True: yield [header, ['>%s %s' % (new, ' '.join(header[1::])), seq[1]]] else: yield ['>%s %s' % (new, ' '.join(header[1::])), seq[1]]
python
def de_rep(fastas, append_index, return_original = False): """ de-replicate fastas based on sequence names """ ids = [] for fasta in fastas: for seq in parse_fasta(fasta): header = seq[0].split('>')[1].split() id = header[0] if id not in ids: ids.append(id) if return_original is True: yield [header, seq] else: yield seq elif append_index == True: new, ids = append_index_id(id, ids) if return_original is True: yield [header, ['>%s %s' % (new, ' '.join(header[1::])), seq[1]]] else: yield ['>%s %s' % (new, ' '.join(header[1::])), seq[1]]
[ "def", "de_rep", "(", "fastas", ",", "append_index", ",", "return_original", "=", "False", ")", ":", "ids", "=", "[", "]", "for", "fasta", "in", "fastas", ":", "for", "seq", "in", "parse_fasta", "(", "fasta", ")", ":", "header", "=", "seq", "[", "0", "]", ".", "split", "(", "'>'", ")", "[", "1", "]", ".", "split", "(", ")", "id", "=", "header", "[", "0", "]", "if", "id", "not", "in", "ids", ":", "ids", ".", "append", "(", "id", ")", "if", "return_original", "is", "True", ":", "yield", "[", "header", ",", "seq", "]", "else", ":", "yield", "seq", "elif", "append_index", "==", "True", ":", "new", ",", "ids", "=", "append_index_id", "(", "id", ",", "ids", ")", "if", "return_original", "is", "True", ":", "yield", "[", "header", ",", "[", "'>%s %s'", "%", "(", "new", ",", "' '", ".", "join", "(", "header", "[", "1", ":", ":", "]", ")", ")", ",", "seq", "[", "1", "]", "]", "]", "else", ":", "yield", "[", "'>%s %s'", "%", "(", "new", ",", "' '", ".", "join", "(", "header", "[", "1", ":", ":", "]", ")", ")", ",", "seq", "[", "1", "]", "]" ]
de-replicate fastas based on sequence names
[ "de", "-", "replicate", "fastas", "based", "on", "sequence", "names" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/nr_fasta.py#L23-L43
train
e-dard/postcodes
postcodes.py
get
def get(postcode): """ Request data associated with `postcode`. :param postcode: the postcode to search for. The postcode may contain spaces (they will be removed). :returns: a dict of the nearest postcode's data or None if no postcode data is found. """ postcode = quote(postcode.replace(' ', '')) url = '%s/postcode/%s.json' % (END_POINT, postcode) return _get_json_resp(url)
python
def get(postcode): """ Request data associated with `postcode`. :param postcode: the postcode to search for. The postcode may contain spaces (they will be removed). :returns: a dict of the nearest postcode's data or None if no postcode data is found. """ postcode = quote(postcode.replace(' ', '')) url = '%s/postcode/%s.json' % (END_POINT, postcode) return _get_json_resp(url)
[ "def", "get", "(", "postcode", ")", ":", "postcode", "=", "quote", "(", "postcode", ".", "replace", "(", "' '", ",", "''", ")", ")", "url", "=", "'%s/postcode/%s.json'", "%", "(", "END_POINT", ",", "postcode", ")", "return", "_get_json_resp", "(", "url", ")" ]
Request data associated with `postcode`. :param postcode: the postcode to search for. The postcode may contain spaces (they will be removed). :returns: a dict of the nearest postcode's data or None if no postcode data is found.
[ "Request", "data", "associated", "with", "postcode", "." ]
d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005
https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L22-L34
train
e-dard/postcodes
postcodes.py
get_from_postcode
def get_from_postcode(postcode, distance): """ Request all postcode data within `distance` miles of `postcode`. :param postcode: the postcode to search for. The postcode may contain spaces (they will be removed). :param distance: distance in miles to `postcode`. :returns: a list of dicts containing postcode data within the specified distance or `None` if `postcode` is not valid. """ postcode = quote(postcode.replace(' ', '')) return _get_from(distance, 'postcode=%s' % postcode)
python
def get_from_postcode(postcode, distance): """ Request all postcode data within `distance` miles of `postcode`. :param postcode: the postcode to search for. The postcode may contain spaces (they will be removed). :param distance: distance in miles to `postcode`. :returns: a list of dicts containing postcode data within the specified distance or `None` if `postcode` is not valid. """ postcode = quote(postcode.replace(' ', '')) return _get_from(distance, 'postcode=%s' % postcode)
[ "def", "get_from_postcode", "(", "postcode", ",", "distance", ")", ":", "postcode", "=", "quote", "(", "postcode", ".", "replace", "(", "' '", ",", "''", ")", ")", "return", "_get_from", "(", "distance", ",", "'postcode=%s'", "%", "postcode", ")" ]
Request all postcode data within `distance` miles of `postcode`. :param postcode: the postcode to search for. The postcode may contain spaces (they will be removed). :param distance: distance in miles to `postcode`. :returns: a list of dicts containing postcode data within the specified distance or `None` if `postcode` is not valid.
[ "Request", "all", "postcode", "data", "within", "distance", "miles", "of", "postcode", "." ]
d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005
https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L56-L69
train
e-dard/postcodes
postcodes.py
PostCoder._check_point
def _check_point(self, lat, lng): """ Checks if latitude and longitude correct """ if abs(lat) > 90 or abs(lng) > 180: msg = "Illegal lat and/or lng, (%s, %s) provided." % (lat, lng) raise IllegalPointException(msg)
python
def _check_point(self, lat, lng): """ Checks if latitude and longitude correct """ if abs(lat) > 90 or abs(lng) > 180: msg = "Illegal lat and/or lng, (%s, %s) provided." % (lat, lng) raise IllegalPointException(msg)
[ "def", "_check_point", "(", "self", ",", "lat", ",", "lng", ")", ":", "if", "abs", "(", "lat", ")", ">", "90", "or", "abs", "(", "lng", ")", ">", "180", ":", "msg", "=", "\"Illegal lat and/or lng, (%s, %s) provided.\"", "%", "(", "lat", ",", "lng", ")", "raise", "IllegalPointException", "(", "msg", ")" ]
Checks if latitude and longitude correct
[ "Checks", "if", "latitude", "and", "longitude", "correct" ]
d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005
https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L123-L127
train
e-dard/postcodes
postcodes.py
PostCoder._lookup
def _lookup(self, skip_cache, fun, *args, **kwargs): """ Checks for cached responses, before requesting from web-service """ if args not in self.cache or skip_cache: self.cache[args] = fun(*args, **kwargs) return self.cache[args]
python
def _lookup(self, skip_cache, fun, *args, **kwargs): """ Checks for cached responses, before requesting from web-service """ if args not in self.cache or skip_cache: self.cache[args] = fun(*args, **kwargs) return self.cache[args]
[ "def", "_lookup", "(", "self", ",", "skip_cache", ",", "fun", ",", "*", "args", ",", "*", "*", "kwargs", ")", ":", "if", "args", "not", "in", "self", ".", "cache", "or", "skip_cache", ":", "self", ".", "cache", "[", "args", "]", "=", "fun", "(", "*", "args", ",", "*", "*", "kwargs", ")", "return", "self", ".", "cache", "[", "args", "]" ]
Checks for cached responses, before requesting from web-service
[ "Checks", "for", "cached", "responses", "before", "requesting", "from", "web", "-", "service" ]
d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005
https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L129-L136
train
e-dard/postcodes
postcodes.py
PostCoder.get_nearest
def get_nearest(self, lat, lng, skip_cache=False): """ Calls `postcodes.get_nearest` but checks correctness of `lat` and `long`, and by default utilises a local cache. :param skip_cache: optional argument specifying whether to skip the cache and make an explicit request. :raises IllegalPointException: if the latitude or longitude are out of bounds. :returns: a dict of the nearest postcode's data. """ lat, lng = float(lat), float(lng) self._check_point(lat, lng) return self._lookup(skip_cache, get_nearest, lat, lng)
python
def get_nearest(self, lat, lng, skip_cache=False): """ Calls `postcodes.get_nearest` but checks correctness of `lat` and `long`, and by default utilises a local cache. :param skip_cache: optional argument specifying whether to skip the cache and make an explicit request. :raises IllegalPointException: if the latitude or longitude are out of bounds. :returns: a dict of the nearest postcode's data. """ lat, lng = float(lat), float(lng) self._check_point(lat, lng) return self._lookup(skip_cache, get_nearest, lat, lng)
[ "def", "get_nearest", "(", "self", ",", "lat", ",", "lng", ",", "skip_cache", "=", "False", ")", ":", "lat", ",", "lng", "=", "float", "(", "lat", ")", ",", "float", "(", "lng", ")", "self", ".", "_check_point", "(", "lat", ",", "lng", ")", "return", "self", ".", "_lookup", "(", "skip_cache", ",", "get_nearest", ",", "lat", ",", "lng", ")" ]
Calls `postcodes.get_nearest` but checks correctness of `lat` and `long`, and by default utilises a local cache. :param skip_cache: optional argument specifying whether to skip the cache and make an explicit request. :raises IllegalPointException: if the latitude or longitude are out of bounds. :returns: a dict of the nearest postcode's data.
[ "Calls", "postcodes", ".", "get_nearest", "but", "checks", "correctness", "of", "lat", "and", "long", "and", "by", "default", "utilises", "a", "local", "cache", "." ]
d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005
https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L152-L167
train
e-dard/postcodes
postcodes.py
PostCoder.get_from_postcode
def get_from_postcode(self, postcode, distance, skip_cache=False): """ Calls `postcodes.get_from_postcode` but checks correctness of `distance`, and by default utilises a local cache. :param skip_cache: optional argument specifying whether to skip the cache and make an explicit request. :raises IllegalPointException: if the latitude or longitude are out of bounds. :returns: a list of dicts containing postcode data within the specified distance. """ distance = float(distance) if distance < 0: raise IllegalDistanceException("Distance must not be negative") # remove spaces and change case here due to caching postcode = postcode.lower().replace(' ', '') return self._lookup(skip_cache, get_from_postcode, postcode, float(distance))
python
def get_from_postcode(self, postcode, distance, skip_cache=False): """ Calls `postcodes.get_from_postcode` but checks correctness of `distance`, and by default utilises a local cache. :param skip_cache: optional argument specifying whether to skip the cache and make an explicit request. :raises IllegalPointException: if the latitude or longitude are out of bounds. :returns: a list of dicts containing postcode data within the specified distance. """ distance = float(distance) if distance < 0: raise IllegalDistanceException("Distance must not be negative") # remove spaces and change case here due to caching postcode = postcode.lower().replace(' ', '') return self._lookup(skip_cache, get_from_postcode, postcode, float(distance))
[ "def", "get_from_postcode", "(", "self", ",", "postcode", ",", "distance", ",", "skip_cache", "=", "False", ")", ":", "distance", "=", "float", "(", "distance", ")", "if", "distance", "<", "0", ":", "raise", "IllegalDistanceException", "(", "\"Distance must not be negative\"", ")", "# remove spaces and change case here due to caching", "postcode", "=", "postcode", ".", "lower", "(", ")", ".", "replace", "(", "' '", ",", "''", ")", "return", "self", ".", "_lookup", "(", "skip_cache", ",", "get_from_postcode", ",", "postcode", ",", "float", "(", "distance", ")", ")" ]
Calls `postcodes.get_from_postcode` but checks correctness of `distance`, and by default utilises a local cache. :param skip_cache: optional argument specifying whether to skip the cache and make an explicit request. :raises IllegalPointException: if the latitude or longitude are out of bounds. :returns: a list of dicts containing postcode data within the specified distance.
[ "Calls", "postcodes", ".", "get_from_postcode", "but", "checks", "correctness", "of", "distance", "and", "by", "default", "utilises", "a", "local", "cache", "." ]
d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005
https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L169-L189
train
e-dard/postcodes
postcodes.py
PostCoder.get_from_geo
def get_from_geo(self, lat, lng, distance, skip_cache=False): """ Calls `postcodes.get_from_geo` but checks the correctness of all arguments, and by default utilises a local cache. :param skip_cache: optional argument specifying whether to skip the cache and make an explicit request. :raises IllegalPointException: if the latitude or longitude are out of bounds. :returns: a list of dicts containing postcode data within the specified distance. """ # remove spaces and change case here due to caching lat, lng, distance = float(lat), float(lng), float(distance) if distance < 0: raise IllegalDistanceException("Distance must not be negative") self._check_point(lat, lng) return self._lookup(skip_cache, get_from_geo, lat, lng, distance)
python
def get_from_geo(self, lat, lng, distance, skip_cache=False): """ Calls `postcodes.get_from_geo` but checks the correctness of all arguments, and by default utilises a local cache. :param skip_cache: optional argument specifying whether to skip the cache and make an explicit request. :raises IllegalPointException: if the latitude or longitude are out of bounds. :returns: a list of dicts containing postcode data within the specified distance. """ # remove spaces and change case here due to caching lat, lng, distance = float(lat), float(lng), float(distance) if distance < 0: raise IllegalDistanceException("Distance must not be negative") self._check_point(lat, lng) return self._lookup(skip_cache, get_from_geo, lat, lng, distance)
[ "def", "get_from_geo", "(", "self", ",", "lat", ",", "lng", ",", "distance", ",", "skip_cache", "=", "False", ")", ":", "# remove spaces and change case here due to caching", "lat", ",", "lng", ",", "distance", "=", "float", "(", "lat", ")", ",", "float", "(", "lng", ")", ",", "float", "(", "distance", ")", "if", "distance", "<", "0", ":", "raise", "IllegalDistanceException", "(", "\"Distance must not be negative\"", ")", "self", ".", "_check_point", "(", "lat", ",", "lng", ")", "return", "self", ".", "_lookup", "(", "skip_cache", ",", "get_from_geo", ",", "lat", ",", "lng", ",", "distance", ")" ]
Calls `postcodes.get_from_geo` but checks the correctness of all arguments, and by default utilises a local cache. :param skip_cache: optional argument specifying whether to skip the cache and make an explicit request. :raises IllegalPointException: if the latitude or longitude are out of bounds. :returns: a list of dicts containing postcode data within the specified distance.
[ "Calls", "postcodes", ".", "get_from_geo", "but", "checks", "the", "correctness", "of", "all", "arguments", "and", "by", "default", "utilises", "a", "local", "cache", "." ]
d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005
https://github.com/e-dard/postcodes/blob/d63c47b4ecd765bc2e4e6ba34bc0b8a796f44005/postcodes.py#L191-L210
train
christophertbrown/bioscripts
ctbBio/rRNA_insertions.py
insertions_from_masked
def insertions_from_masked(seq): """ get coordinates of insertions from insertion-masked sequence """ insertions = [] prev = True for i, base in enumerate(seq): if base.isupper() and prev is True: insertions.append([]) prev = False elif base.islower(): insertions[-1].append(i) prev = True return [[min(i), max(i)] for i in insertions if i != []]
python
def insertions_from_masked(seq): """ get coordinates of insertions from insertion-masked sequence """ insertions = [] prev = True for i, base in enumerate(seq): if base.isupper() and prev is True: insertions.append([]) prev = False elif base.islower(): insertions[-1].append(i) prev = True return [[min(i), max(i)] for i in insertions if i != []]
[ "def", "insertions_from_masked", "(", "seq", ")", ":", "insertions", "=", "[", "]", "prev", "=", "True", "for", "i", ",", "base", "in", "enumerate", "(", "seq", ")", ":", "if", "base", ".", "isupper", "(", ")", "and", "prev", "is", "True", ":", "insertions", ".", "append", "(", "[", "]", ")", "prev", "=", "False", "elif", "base", ".", "islower", "(", ")", ":", "insertions", "[", "-", "1", "]", ".", "append", "(", "i", ")", "prev", "=", "True", "return", "[", "[", "min", "(", "i", ")", ",", "max", "(", "i", ")", "]", "for", "i", "in", "insertions", "if", "i", "!=", "[", "]", "]" ]
get coordinates of insertions from insertion-masked sequence
[ "get", "coordinates", "of", "insertions", "from", "insertion", "-", "masked", "sequence" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L15-L28
train
christophertbrown/bioscripts
ctbBio/rRNA_insertions.py
seq_info
def seq_info(names, id2names, insertions, sequences): """ get insertion information from header """ seqs = {} # seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]] for name in names: id = id2names[name] gene = name.split('fromHMM::', 1)[0].rsplit(' ', 1)[1] model = name.split('fromHMM::', 1)[1].split('=', 1)[1].split()[0] i_gene_pos = insertions[id] # coordinates of each insertion wrt gene i_model_pos = name.split('fromHMM::', 1)[1].split('model-pos(ins-len)=')[1].split()[0].split(';') # model overlap i_info = [] for i, ins in enumerate(i_gene_pos): model_pos = i_model_pos[i].split('-')[1].split('(')[0] length = i_model_pos[i].split('(')[1].split(')')[0] iheader = '>%s_%s insertion::seq=%s type=insertion strand=n/a gene-pos=%s-%s model-pos=%s'\ % (id, (i + 1), (i + 1), ins[0], ins[1], model_pos) iseq = sequences[id][1][ins[0]:(ins[1] + 1)] iseq = [iheader, iseq] info = [ins, model_pos, length, iseq, [], []] i_info.append(info) seqs[id] = [gene, model, i_info] return seqs
python
def seq_info(names, id2names, insertions, sequences): """ get insertion information from header """ seqs = {} # seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]] for name in names: id = id2names[name] gene = name.split('fromHMM::', 1)[0].rsplit(' ', 1)[1] model = name.split('fromHMM::', 1)[1].split('=', 1)[1].split()[0] i_gene_pos = insertions[id] # coordinates of each insertion wrt gene i_model_pos = name.split('fromHMM::', 1)[1].split('model-pos(ins-len)=')[1].split()[0].split(';') # model overlap i_info = [] for i, ins in enumerate(i_gene_pos): model_pos = i_model_pos[i].split('-')[1].split('(')[0] length = i_model_pos[i].split('(')[1].split(')')[0] iheader = '>%s_%s insertion::seq=%s type=insertion strand=n/a gene-pos=%s-%s model-pos=%s'\ % (id, (i + 1), (i + 1), ins[0], ins[1], model_pos) iseq = sequences[id][1][ins[0]:(ins[1] + 1)] iseq = [iheader, iseq] info = [ins, model_pos, length, iseq, [], []] i_info.append(info) seqs[id] = [gene, model, i_info] return seqs
[ "def", "seq_info", "(", "names", ",", "id2names", ",", "insertions", ",", "sequences", ")", ":", "seqs", "=", "{", "}", "# seqs[id] = [gene, model, [[i-gene_pos, i-model_pos, i-length, iseq, [orfs], [introns]], ...]]", "for", "name", "in", "names", ":", "id", "=", "id2names", "[", "name", "]", "gene", "=", "name", ".", "split", "(", "'fromHMM::'", ",", "1", ")", "[", "0", "]", ".", "rsplit", "(", "' '", ",", "1", ")", "[", "1", "]", "model", "=", "name", ".", "split", "(", "'fromHMM::'", ",", "1", ")", "[", "1", "]", ".", "split", "(", "'='", ",", "1", ")", "[", "1", "]", ".", "split", "(", ")", "[", "0", "]", "i_gene_pos", "=", "insertions", "[", "id", "]", "# coordinates of each insertion wrt gene", "i_model_pos", "=", "name", ".", "split", "(", "'fromHMM::'", ",", "1", ")", "[", "1", "]", ".", "split", "(", "'model-pos(ins-len)='", ")", "[", "1", "]", ".", "split", "(", ")", "[", "0", "]", ".", "split", "(", "';'", ")", "# model overlap", "i_info", "=", "[", "]", "for", "i", ",", "ins", "in", "enumerate", "(", "i_gene_pos", ")", ":", "model_pos", "=", "i_model_pos", "[", "i", "]", ".", "split", "(", "'-'", ")", "[", "1", "]", ".", "split", "(", "'('", ")", "[", "0", "]", "length", "=", "i_model_pos", "[", "i", "]", ".", "split", "(", "'('", ")", "[", "1", "]", ".", "split", "(", "')'", ")", "[", "0", "]", "iheader", "=", "'>%s_%s insertion::seq=%s type=insertion strand=n/a gene-pos=%s-%s model-pos=%s'", "%", "(", "id", ",", "(", "i", "+", "1", ")", ",", "(", "i", "+", "1", ")", ",", "ins", "[", "0", "]", ",", "ins", "[", "1", "]", ",", "model_pos", ")", "iseq", "=", "sequences", "[", "id", "]", "[", "1", "]", "[", "ins", "[", "0", "]", ":", "(", "ins", "[", "1", "]", "+", "1", ")", "]", "iseq", "=", "[", "iheader", ",", "iseq", "]", "info", "=", "[", "ins", ",", "model_pos", ",", "length", ",", "iseq", ",", "[", "]", ",", "[", "]", "]", "i_info", ".", "append", "(", "info", ")", "seqs", "[", "id", "]", "=", "[", "gene", ",", "model", ",", "i_info", "]", "return", "seqs" ]
get insertion information from header
[ "get", "insertion", "information", "from", "header" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L64-L86
train
christophertbrown/bioscripts
ctbBio/rRNA_insertions.py
check_overlap
def check_overlap(pos, ins, thresh): """ make sure thresh % feature is contained within insertion """ ins_pos = ins[0] ins_len = ins[2] ol = overlap(ins_pos, pos) feat_len = pos[1] - pos[0] + 1 # print float(ol) / float(feat_len) if float(ol) / float(feat_len) >= thresh: return True return False
python
def check_overlap(pos, ins, thresh): """ make sure thresh % feature is contained within insertion """ ins_pos = ins[0] ins_len = ins[2] ol = overlap(ins_pos, pos) feat_len = pos[1] - pos[0] + 1 # print float(ol) / float(feat_len) if float(ol) / float(feat_len) >= thresh: return True return False
[ "def", "check_overlap", "(", "pos", ",", "ins", ",", "thresh", ")", ":", "ins_pos", "=", "ins", "[", "0", "]", "ins_len", "=", "ins", "[", "2", "]", "ol", "=", "overlap", "(", "ins_pos", ",", "pos", ")", "feat_len", "=", "pos", "[", "1", "]", "-", "pos", "[", "0", "]", "+", "1", "# print float(ol) / float(feat_len)", "if", "float", "(", "ol", ")", "/", "float", "(", "feat_len", ")", ">=", "thresh", ":", "return", "True", "return", "False" ]
make sure thresh % feature is contained within insertion
[ "make", "sure", "thresh", "%", "feature", "is", "contained", "within", "insertion" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L91-L102
train
christophertbrown/bioscripts
ctbBio/rRNA_insertions.py
max_insertion
def max_insertion(seqs, gene, domain): """ length of largest insertion """ seqs = [i[2] for i in list(seqs.values()) if i[2] != [] and i[0] == gene and i[1] == domain] lengths = [] for seq in seqs: for ins in seq: lengths.append(int(ins[2])) if lengths == []: return 100 return max(lengths)
python
def max_insertion(seqs, gene, domain): """ length of largest insertion """ seqs = [i[2] for i in list(seqs.values()) if i[2] != [] and i[0] == gene and i[1] == domain] lengths = [] for seq in seqs: for ins in seq: lengths.append(int(ins[2])) if lengths == []: return 100 return max(lengths)
[ "def", "max_insertion", "(", "seqs", ",", "gene", ",", "domain", ")", ":", "seqs", "=", "[", "i", "[", "2", "]", "for", "i", "in", "list", "(", "seqs", ".", "values", "(", ")", ")", "if", "i", "[", "2", "]", "!=", "[", "]", "and", "i", "[", "0", "]", "==", "gene", "and", "i", "[", "1", "]", "==", "domain", "]", "lengths", "=", "[", "]", "for", "seq", "in", "seqs", ":", "for", "ins", "in", "seq", ":", "lengths", ".", "append", "(", "int", "(", "ins", "[", "2", "]", ")", ")", "if", "lengths", "==", "[", "]", ":", "return", "100", "return", "max", "(", "lengths", ")" ]
length of largest insertion
[ "length", "of", "largest", "insertion" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L305-L316
train
christophertbrown/bioscripts
ctbBio/rRNA_insertions.py
model_length
def model_length(gene, domain): """ get length of model """ if gene == '16S': domain2max = {'E_coli_K12': int(1538), 'bacteria': int(1689), 'archaea': int(1563), 'eukarya': int(2652)} return domain2max[domain] elif gene == '23S': domain2max = {'E_coli_K12': int(2903), 'bacteria': int(3146), 'archaea': int(3774), 'eukarya': int(9079)} return domain2max[domain] else: print(sys.stderr, '# length unknown for gene: %s, domain: %s' % (gene, domain)) exit()
python
def model_length(gene, domain): """ get length of model """ if gene == '16S': domain2max = {'E_coli_K12': int(1538), 'bacteria': int(1689), 'archaea': int(1563), 'eukarya': int(2652)} return domain2max[domain] elif gene == '23S': domain2max = {'E_coli_K12': int(2903), 'bacteria': int(3146), 'archaea': int(3774), 'eukarya': int(9079)} return domain2max[domain] else: print(sys.stderr, '# length unknown for gene: %s, domain: %s' % (gene, domain)) exit()
[ "def", "model_length", "(", "gene", ",", "domain", ")", ":", "if", "gene", "==", "'16S'", ":", "domain2max", "=", "{", "'E_coli_K12'", ":", "int", "(", "1538", ")", ",", "'bacteria'", ":", "int", "(", "1689", ")", ",", "'archaea'", ":", "int", "(", "1563", ")", ",", "'eukarya'", ":", "int", "(", "2652", ")", "}", "return", "domain2max", "[", "domain", "]", "elif", "gene", "==", "'23S'", ":", "domain2max", "=", "{", "'E_coli_K12'", ":", "int", "(", "2903", ")", ",", "'bacteria'", ":", "int", "(", "3146", ")", ",", "'archaea'", ":", "int", "(", "3774", ")", ",", "'eukarya'", ":", "int", "(", "9079", ")", "}", "return", "domain2max", "[", "domain", "]", "else", ":", "print", "(", "sys", ".", "stderr", ",", "'# length unknown for gene: %s, domain: %s'", "%", "(", "gene", ",", "domain", ")", ")", "exit", "(", ")" ]
get length of model
[ "get", "length", "of", "model" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L318-L330
train
christophertbrown/bioscripts
ctbBio/rRNA_insertions.py
setup_markers
def setup_markers(seqs): """ setup unique marker for every orf annotation - change size if necessary """ family2marker = {} # family2marker[family] = [marker, size] markers = cycle(['^', 'p', '*', '+', 'x', 'd', '|', 'v', '>', '<', '8']) size = 60 families = [] for seq in list(seqs.values()): for insertion in seq[2]: for family in list(insertion[-1].values()): if family not in families: families.append(family) for family in families: marker = next(markers) if marker == '^': size = size * 0.5 family2marker[family] = [marker, size] return family2marker
python
def setup_markers(seqs): """ setup unique marker for every orf annotation - change size if necessary """ family2marker = {} # family2marker[family] = [marker, size] markers = cycle(['^', 'p', '*', '+', 'x', 'd', '|', 'v', '>', '<', '8']) size = 60 families = [] for seq in list(seqs.values()): for insertion in seq[2]: for family in list(insertion[-1].values()): if family not in families: families.append(family) for family in families: marker = next(markers) if marker == '^': size = size * 0.5 family2marker[family] = [marker, size] return family2marker
[ "def", "setup_markers", "(", "seqs", ")", ":", "family2marker", "=", "{", "}", "# family2marker[family] = [marker, size]", "markers", "=", "cycle", "(", "[", "'^'", ",", "'p'", ",", "'*'", ",", "'+'", ",", "'x'", ",", "'d'", ",", "'|'", ",", "'v'", ",", "'>'", ",", "'<'", ",", "'8'", "]", ")", "size", "=", "60", "families", "=", "[", "]", "for", "seq", "in", "list", "(", "seqs", ".", "values", "(", ")", ")", ":", "for", "insertion", "in", "seq", "[", "2", "]", ":", "for", "family", "in", "list", "(", "insertion", "[", "-", "1", "]", ".", "values", "(", ")", ")", ":", "if", "family", "not", "in", "families", ":", "families", ".", "append", "(", "family", ")", "for", "family", "in", "families", ":", "marker", "=", "next", "(", "markers", ")", "if", "marker", "==", "'^'", ":", "size", "=", "size", "*", "0.5", "family2marker", "[", "family", "]", "=", "[", "marker", ",", "size", "]", "return", "family2marker" ]
setup unique marker for every orf annotation - change size if necessary
[ "setup", "unique", "marker", "for", "every", "orf", "annotation", "-", "change", "size", "if", "necessary" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L332-L351
train
christophertbrown/bioscripts
ctbBio/rRNA_insertions.py
plot_by_gene_and_domain
def plot_by_gene_and_domain(name, seqs, tax, id2name): """ plot insertions for each gene and domain """ for gene in set([seq[0] for seq in list(seqs.values())]): for domain in set([seq[1] for seq in list(seqs.values())]): plot_insertions(name, seqs, gene, domain, tax, id2name)
python
def plot_by_gene_and_domain(name, seqs, tax, id2name): """ plot insertions for each gene and domain """ for gene in set([seq[0] for seq in list(seqs.values())]): for domain in set([seq[1] for seq in list(seqs.values())]): plot_insertions(name, seqs, gene, domain, tax, id2name)
[ "def", "plot_by_gene_and_domain", "(", "name", ",", "seqs", ",", "tax", ",", "id2name", ")", ":", "for", "gene", "in", "set", "(", "[", "seq", "[", "0", "]", "for", "seq", "in", "list", "(", "seqs", ".", "values", "(", ")", ")", "]", ")", ":", "for", "domain", "in", "set", "(", "[", "seq", "[", "1", "]", "for", "seq", "in", "list", "(", "seqs", ".", "values", "(", ")", ")", "]", ")", ":", "plot_insertions", "(", "name", ",", "seqs", ",", "gene", ",", "domain", ",", "tax", ",", "id2name", ")" ]
plot insertions for each gene and domain
[ "plot", "insertions", "for", "each", "gene", "and", "domain" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rRNA_insertions.py#L551-L557
train
christophertbrown/bioscripts
ctbBio/neto.py
get_descriptions
def get_descriptions(fastas): """ get the description for each ORF """ id2desc = {} for fasta in fastas: for seq in parse_fasta(fasta): header = seq[0].split('>')[1].split(' ') id = header[0] if len(header) > 1: desc = ' '.join(header[1:]) else: desc = 'n/a' length = float(len([i for i in seq[1].strip() if i != '*'])) id2desc[id] = [fasta, desc, length] return id2desc
python
def get_descriptions(fastas): """ get the description for each ORF """ id2desc = {} for fasta in fastas: for seq in parse_fasta(fasta): header = seq[0].split('>')[1].split(' ') id = header[0] if len(header) > 1: desc = ' '.join(header[1:]) else: desc = 'n/a' length = float(len([i for i in seq[1].strip() if i != '*'])) id2desc[id] = [fasta, desc, length] return id2desc
[ "def", "get_descriptions", "(", "fastas", ")", ":", "id2desc", "=", "{", "}", "for", "fasta", "in", "fastas", ":", "for", "seq", "in", "parse_fasta", "(", "fasta", ")", ":", "header", "=", "seq", "[", "0", "]", ".", "split", "(", "'>'", ")", "[", "1", "]", ".", "split", "(", "' '", ")", "id", "=", "header", "[", "0", "]", "if", "len", "(", "header", ")", ">", "1", ":", "desc", "=", "' '", ".", "join", "(", "header", "[", "1", ":", "]", ")", "else", ":", "desc", "=", "'n/a'", "length", "=", "float", "(", "len", "(", "[", "i", "for", "i", "in", "seq", "[", "1", "]", ".", "strip", "(", ")", "if", "i", "!=", "'*'", "]", ")", ")", "id2desc", "[", "id", "]", "=", "[", "fasta", ",", "desc", ",", "length", "]", "return", "id2desc" ]
get the description for each ORF
[ "get", "the", "description", "for", "each", "ORF" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L37-L52
train
christophertbrown/bioscripts
ctbBio/neto.py
print_genome_matrix
def print_genome_matrix(hits, fastas, id2desc, file_name): """ optimize later? slow ... should combine with calculate_threshold module """ out = open(file_name, 'w') fastas = sorted(fastas) print('## percent identity between genomes', file=out) print('# - \t %s' % ('\t'.join(fastas)), file=out) for fasta in fastas: line = [fasta] for other in fastas: if other == fasta: average = '-' else: average = numpy.average([hits[fasta][other][i][3] for i in hits[fasta][other]]) line.append(str(average)) print('\t'.join(line), file=out) print('', file=out) print('## percent of orfs that are orthologous between genomes', file=out) print('# - \t %s' % ('\t'.join(fastas)), file=out) for fasta in fastas: line = [fasta] for other in fastas: if other == fasta: percent = '-' else: orthologs = float(len(hits[fasta][other])) orfs = float(len([i for i in id2desc if id2desc[i][0] == fasta])) percent = float(orthologs / orfs) * 100 line.append(str(percent)) print('\t'.join(line), file=out)
python
def print_genome_matrix(hits, fastas, id2desc, file_name): """ optimize later? slow ... should combine with calculate_threshold module """ out = open(file_name, 'w') fastas = sorted(fastas) print('## percent identity between genomes', file=out) print('# - \t %s' % ('\t'.join(fastas)), file=out) for fasta in fastas: line = [fasta] for other in fastas: if other == fasta: average = '-' else: average = numpy.average([hits[fasta][other][i][3] for i in hits[fasta][other]]) line.append(str(average)) print('\t'.join(line), file=out) print('', file=out) print('## percent of orfs that are orthologous between genomes', file=out) print('# - \t %s' % ('\t'.join(fastas)), file=out) for fasta in fastas: line = [fasta] for other in fastas: if other == fasta: percent = '-' else: orthologs = float(len(hits[fasta][other])) orfs = float(len([i for i in id2desc if id2desc[i][0] == fasta])) percent = float(orthologs / orfs) * 100 line.append(str(percent)) print('\t'.join(line), file=out)
[ "def", "print_genome_matrix", "(", "hits", ",", "fastas", ",", "id2desc", ",", "file_name", ")", ":", "out", "=", "open", "(", "file_name", ",", "'w'", ")", "fastas", "=", "sorted", "(", "fastas", ")", "print", "(", "'## percent identity between genomes'", ",", "file", "=", "out", ")", "print", "(", "'# - \\t %s'", "%", "(", "'\\t'", ".", "join", "(", "fastas", ")", ")", ",", "file", "=", "out", ")", "for", "fasta", "in", "fastas", ":", "line", "=", "[", "fasta", "]", "for", "other", "in", "fastas", ":", "if", "other", "==", "fasta", ":", "average", "=", "'-'", "else", ":", "average", "=", "numpy", ".", "average", "(", "[", "hits", "[", "fasta", "]", "[", "other", "]", "[", "i", "]", "[", "3", "]", "for", "i", "in", "hits", "[", "fasta", "]", "[", "other", "]", "]", ")", "line", ".", "append", "(", "str", "(", "average", ")", ")", "print", "(", "'\\t'", ".", "join", "(", "line", ")", ",", "file", "=", "out", ")", "print", "(", "''", ",", "file", "=", "out", ")", "print", "(", "'## percent of orfs that are orthologous between genomes'", ",", "file", "=", "out", ")", "print", "(", "'# - \\t %s'", "%", "(", "'\\t'", ".", "join", "(", "fastas", ")", ")", ",", "file", "=", "out", ")", "for", "fasta", "in", "fastas", ":", "line", "=", "[", "fasta", "]", "for", "other", "in", "fastas", ":", "if", "other", "==", "fasta", ":", "percent", "=", "'-'", "else", ":", "orthologs", "=", "float", "(", "len", "(", "hits", "[", "fasta", "]", "[", "other", "]", ")", ")", "orfs", "=", "float", "(", "len", "(", "[", "i", "for", "i", "in", "id2desc", "if", "id2desc", "[", "i", "]", "[", "0", "]", "==", "fasta", "]", ")", ")", "percent", "=", "float", "(", "orthologs", "/", "orfs", ")", "*", "100", "line", ".", "append", "(", "str", "(", "percent", ")", ")", "print", "(", "'\\t'", ".", "join", "(", "line", ")", ",", "file", "=", "out", ")" ]
optimize later? slow ... should combine with calculate_threshold module
[ "optimize", "later?", "slow", "...", "should", "combine", "with", "calculate_threshold", "module" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L140-L171
train
christophertbrown/bioscripts
ctbBio/neto.py
self_compare
def self_compare(fastas, id2desc, algorithm): """ compare genome to self to get the best possible bit score for each ORF """ for fasta in fastas: blast = open(search(fasta, fasta, method = algorithm, alignment = 'local')) for hit in best_blast(blast, 1): id, bit = hit[0].split()[0], float(hit[-1]) id2desc[id].append(bit) return id2desc
python
def self_compare(fastas, id2desc, algorithm): """ compare genome to self to get the best possible bit score for each ORF """ for fasta in fastas: blast = open(search(fasta, fasta, method = algorithm, alignment = 'local')) for hit in best_blast(blast, 1): id, bit = hit[0].split()[0], float(hit[-1]) id2desc[id].append(bit) return id2desc
[ "def", "self_compare", "(", "fastas", ",", "id2desc", ",", "algorithm", ")", ":", "for", "fasta", "in", "fastas", ":", "blast", "=", "open", "(", "search", "(", "fasta", ",", "fasta", ",", "method", "=", "algorithm", ",", "alignment", "=", "'local'", ")", ")", "for", "hit", "in", "best_blast", "(", "blast", ",", "1", ")", ":", "id", ",", "bit", "=", "hit", "[", "0", "]", ".", "split", "(", ")", "[", "0", "]", ",", "float", "(", "hit", "[", "-", "1", "]", ")", "id2desc", "[", "id", "]", ".", "append", "(", "bit", ")", "return", "id2desc" ]
compare genome to self to get the best possible bit score for each ORF
[ "compare", "genome", "to", "self", "to", "get", "the", "best", "possible", "bit", "score", "for", "each", "ORF" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L240-L249
train
christophertbrown/bioscripts
ctbBio/neto.py
calc_thresholds
def calc_thresholds(rbh, file_name, thresholds = [False, False, False, False], stdevs = 2): """ if thresholds are not specififed, calculate based on the distribution of normalized bit scores """ calc_threshold = thresholds[-1] norm_threshold = {} for pair in itertools.permutations([i for i in rbh], 2): if pair[0] not in norm_threshold: norm_threshold[pair[0]] = {} norm_threshold[pair[0]][pair[1]] = {} out = open(file_name, 'w') print('#### summary of rbh comparisons\n', file=out) comparisons = [] for genome in rbh: for compare in rbh[genome]: pair = ''.join(sorted([genome, compare])) if pair in comparisons: continue comparisons.append(pair) scores = {'percent identity': [], 'e-value': [], 'bit score': [], 'normalized bit score': [], 'alignment length fraction': []} print('### blast between %s and %s\n' % (genome, compare), file=out) for id in rbh[genome][compare]: pident, length_fraction, e, bit, norm_bit = rbh[genome][compare][id][3:] scores['percent identity'].append(pident) scores['alignment length fraction'].append(length_fraction) scores['e-value'].append(e) scores['bit score'].append(bit) scores['normalized bit score'].append(norm_bit) if calc_threshold is True: norms = scores['normalized bit score'] average = numpy.average(norms) std = numpy.std(norms) normal_thresh = average - (std * stdevs) print('## average normalized bit score: %s' % average, file=out) print('## standard deviation of normalized bit scores: %s' % std, file=out) print('## normalized bit score threshold set to: %s\n' % (normal_thresh), file=out) norm_threshold[genome][compare], norm_threshold[compare][genome] = normal_thresh, normal_thresh for score in scores: print('## %s' % (score), file=out) if len(scores[score]) > 0: print('## average: %s' % numpy.average(scores[score]), file=out) # hist = histogram(scores[score], []) # for line in hist: # print >> out, line print('', file=out) out.close() if calc_threshold is True: return thresholds[0:-1] + [norm_threshold] else: return thresholds
python
def calc_thresholds(rbh, file_name, thresholds = [False, False, False, False], stdevs = 2): """ if thresholds are not specififed, calculate based on the distribution of normalized bit scores """ calc_threshold = thresholds[-1] norm_threshold = {} for pair in itertools.permutations([i for i in rbh], 2): if pair[0] not in norm_threshold: norm_threshold[pair[0]] = {} norm_threshold[pair[0]][pair[1]] = {} out = open(file_name, 'w') print('#### summary of rbh comparisons\n', file=out) comparisons = [] for genome in rbh: for compare in rbh[genome]: pair = ''.join(sorted([genome, compare])) if pair in comparisons: continue comparisons.append(pair) scores = {'percent identity': [], 'e-value': [], 'bit score': [], 'normalized bit score': [], 'alignment length fraction': []} print('### blast between %s and %s\n' % (genome, compare), file=out) for id in rbh[genome][compare]: pident, length_fraction, e, bit, norm_bit = rbh[genome][compare][id][3:] scores['percent identity'].append(pident) scores['alignment length fraction'].append(length_fraction) scores['e-value'].append(e) scores['bit score'].append(bit) scores['normalized bit score'].append(norm_bit) if calc_threshold is True: norms = scores['normalized bit score'] average = numpy.average(norms) std = numpy.std(norms) normal_thresh = average - (std * stdevs) print('## average normalized bit score: %s' % average, file=out) print('## standard deviation of normalized bit scores: %s' % std, file=out) print('## normalized bit score threshold set to: %s\n' % (normal_thresh), file=out) norm_threshold[genome][compare], norm_threshold[compare][genome] = normal_thresh, normal_thresh for score in scores: print('## %s' % (score), file=out) if len(scores[score]) > 0: print('## average: %s' % numpy.average(scores[score]), file=out) # hist = histogram(scores[score], []) # for line in hist: # print >> out, line print('', file=out) out.close() if calc_threshold is True: return thresholds[0:-1] + [norm_threshold] else: return thresholds
[ "def", "calc_thresholds", "(", "rbh", ",", "file_name", ",", "thresholds", "=", "[", "False", ",", "False", ",", "False", ",", "False", "]", ",", "stdevs", "=", "2", ")", ":", "calc_threshold", "=", "thresholds", "[", "-", "1", "]", "norm_threshold", "=", "{", "}", "for", "pair", "in", "itertools", ".", "permutations", "(", "[", "i", "for", "i", "in", "rbh", "]", ",", "2", ")", ":", "if", "pair", "[", "0", "]", "not", "in", "norm_threshold", ":", "norm_threshold", "[", "pair", "[", "0", "]", "]", "=", "{", "}", "norm_threshold", "[", "pair", "[", "0", "]", "]", "[", "pair", "[", "1", "]", "]", "=", "{", "}", "out", "=", "open", "(", "file_name", ",", "'w'", ")", "print", "(", "'#### summary of rbh comparisons\\n'", ",", "file", "=", "out", ")", "comparisons", "=", "[", "]", "for", "genome", "in", "rbh", ":", "for", "compare", "in", "rbh", "[", "genome", "]", ":", "pair", "=", "''", ".", "join", "(", "sorted", "(", "[", "genome", ",", "compare", "]", ")", ")", "if", "pair", "in", "comparisons", ":", "continue", "comparisons", ".", "append", "(", "pair", ")", "scores", "=", "{", "'percent identity'", ":", "[", "]", ",", "'e-value'", ":", "[", "]", ",", "'bit score'", ":", "[", "]", ",", "'normalized bit score'", ":", "[", "]", ",", "'alignment length fraction'", ":", "[", "]", "}", "print", "(", "'### blast between %s and %s\\n'", "%", "(", "genome", ",", "compare", ")", ",", "file", "=", "out", ")", "for", "id", "in", "rbh", "[", "genome", "]", "[", "compare", "]", ":", "pident", ",", "length_fraction", ",", "e", ",", "bit", ",", "norm_bit", "=", "rbh", "[", "genome", "]", "[", "compare", "]", "[", "id", "]", "[", "3", ":", "]", "scores", "[", "'percent identity'", "]", ".", "append", "(", "pident", ")", "scores", "[", "'alignment length fraction'", "]", ".", "append", "(", "length_fraction", ")", "scores", "[", "'e-value'", "]", ".", "append", "(", "e", ")", "scores", "[", "'bit score'", "]", ".", "append", "(", "bit", ")", "scores", "[", "'normalized bit score'", "]", ".", "append", "(", "norm_bit", ")", "if", "calc_threshold", "is", "True", ":", "norms", "=", "scores", "[", "'normalized bit score'", "]", "average", "=", "numpy", ".", "average", "(", "norms", ")", "std", "=", "numpy", ".", "std", "(", "norms", ")", "normal_thresh", "=", "average", "-", "(", "std", "*", "stdevs", ")", "print", "(", "'## average normalized bit score: %s'", "%", "average", ",", "file", "=", "out", ")", "print", "(", "'## standard deviation of normalized bit scores: %s'", "%", "std", ",", "file", "=", "out", ")", "print", "(", "'## normalized bit score threshold set to: %s\\n'", "%", "(", "normal_thresh", ")", ",", "file", "=", "out", ")", "norm_threshold", "[", "genome", "]", "[", "compare", "]", ",", "norm_threshold", "[", "compare", "]", "[", "genome", "]", "=", "normal_thresh", ",", "normal_thresh", "for", "score", "in", "scores", ":", "print", "(", "'## %s'", "%", "(", "score", ")", ",", "file", "=", "out", ")", "if", "len", "(", "scores", "[", "score", "]", ")", ">", "0", ":", "print", "(", "'## average: %s'", "%", "numpy", ".", "average", "(", "scores", "[", "score", "]", ")", ",", "file", "=", "out", ")", "# hist = histogram(scores[score], [])", "# for line in hist:", "# print >> out, line", "print", "(", "''", ",", "file", "=", "out", ")", "out", ".", "close", "(", ")", "if", "calc_threshold", "is", "True", ":", "return", "thresholds", "[", "0", ":", "-", "1", "]", "+", "[", "norm_threshold", "]", "else", ":", "return", "thresholds" ]
if thresholds are not specififed, calculate based on the distribution of normalized bit scores
[ "if", "thresholds", "are", "not", "specififed", "calculate", "based", "on", "the", "distribution", "of", "normalized", "bit", "scores" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L303-L352
train
christophertbrown/bioscripts
ctbBio/neto.py
neto
def neto(fastas, algorithm = 'usearch', e = 0.01, bit = 40, length = .65, norm_bit = False): """ make and split a rbh network """ thresholds = [e, bit, length, norm_bit] id2desc = get_descriptions(fastas) # get [fasta, description, length] for ORF id id2desc = self_compare(fastas, id2desc, algorithm) # get best possible bit score for each ORF # (comparing with itself) [fasta, description, length, bestbit] hits = compare_genomes(fastas, id2desc, algorithm) # pair wise genome comparisons {genome: {id: [match_type = 'rbh' or 'fbh', scores]}} calc_thresholds(hits, file_name = 'fbh.scores.summary.txt') rbh_network(id2desc, hits, file_name = 'fbh.network.edges.txt') hits, rbh = find_rbh(hits, id2desc) # remove hits that are not reciprocal best blast hits thresholds = calc_thresholds(rbh, 'rbh.scores.summary.txt', thresholds) # print rbh score summary to rbh_score_summary.txt and # calculate normalized bit score cutoff for each pair of # genomes, if desired g = rbh_network(id2desc, rbh, file_name = 'rbh.network.edges.txt') filtered_g, filtered_rbh = rbh_network(id2desc, rbh, 'rbh.filtered.network.edges.txt', thresholds) calc_thresholds(filtered_rbh, file_name = 'rbh.filtered.scores.summary.txt') print_summary(filtered_g, fastas, id2desc, file_name = 'rbh.filtered.network.nodes.txt') print_network_matrix(filtered_g, fastas, id2desc, file_name = 'rbh.filtered.network.matrix.txt') print_genome_matrix(filtered_rbh, fastas, id2desc, file_name = 'rbh.filtered.network.genome_matrix.txt') split_g = split_network(filtered_g, id2desc, file_name = 'rbh.filtered.split.network.edges.txt') print_summary(split_g, fastas, id2desc, file_name = 'rbh.filtered.split.network.nodes.txt') print_network_matrix(split_g, fastas, id2desc, file_name = 'rbh.filtered.split.network.matrix.txt') return split_g
python
def neto(fastas, algorithm = 'usearch', e = 0.01, bit = 40, length = .65, norm_bit = False): """ make and split a rbh network """ thresholds = [e, bit, length, norm_bit] id2desc = get_descriptions(fastas) # get [fasta, description, length] for ORF id id2desc = self_compare(fastas, id2desc, algorithm) # get best possible bit score for each ORF # (comparing with itself) [fasta, description, length, bestbit] hits = compare_genomes(fastas, id2desc, algorithm) # pair wise genome comparisons {genome: {id: [match_type = 'rbh' or 'fbh', scores]}} calc_thresholds(hits, file_name = 'fbh.scores.summary.txt') rbh_network(id2desc, hits, file_name = 'fbh.network.edges.txt') hits, rbh = find_rbh(hits, id2desc) # remove hits that are not reciprocal best blast hits thresholds = calc_thresholds(rbh, 'rbh.scores.summary.txt', thresholds) # print rbh score summary to rbh_score_summary.txt and # calculate normalized bit score cutoff for each pair of # genomes, if desired g = rbh_network(id2desc, rbh, file_name = 'rbh.network.edges.txt') filtered_g, filtered_rbh = rbh_network(id2desc, rbh, 'rbh.filtered.network.edges.txt', thresholds) calc_thresholds(filtered_rbh, file_name = 'rbh.filtered.scores.summary.txt') print_summary(filtered_g, fastas, id2desc, file_name = 'rbh.filtered.network.nodes.txt') print_network_matrix(filtered_g, fastas, id2desc, file_name = 'rbh.filtered.network.matrix.txt') print_genome_matrix(filtered_rbh, fastas, id2desc, file_name = 'rbh.filtered.network.genome_matrix.txt') split_g = split_network(filtered_g, id2desc, file_name = 'rbh.filtered.split.network.edges.txt') print_summary(split_g, fastas, id2desc, file_name = 'rbh.filtered.split.network.nodes.txt') print_network_matrix(split_g, fastas, id2desc, file_name = 'rbh.filtered.split.network.matrix.txt') return split_g
[ "def", "neto", "(", "fastas", ",", "algorithm", "=", "'usearch'", ",", "e", "=", "0.01", ",", "bit", "=", "40", ",", "length", "=", ".65", ",", "norm_bit", "=", "False", ")", ":", "thresholds", "=", "[", "e", ",", "bit", ",", "length", ",", "norm_bit", "]", "id2desc", "=", "get_descriptions", "(", "fastas", ")", "# get [fasta, description, length] for ORF id", "id2desc", "=", "self_compare", "(", "fastas", ",", "id2desc", ",", "algorithm", ")", "# get best possible bit score for each ORF ", "# (comparing with itself) [fasta, description, length, bestbit]", "hits", "=", "compare_genomes", "(", "fastas", ",", "id2desc", ",", "algorithm", ")", "# pair wise genome comparisons {genome: {id: [match_type = 'rbh' or 'fbh', scores]}}", "calc_thresholds", "(", "hits", ",", "file_name", "=", "'fbh.scores.summary.txt'", ")", "rbh_network", "(", "id2desc", ",", "hits", ",", "file_name", "=", "'fbh.network.edges.txt'", ")", "hits", ",", "rbh", "=", "find_rbh", "(", "hits", ",", "id2desc", ")", "# remove hits that are not reciprocal best blast hits", "thresholds", "=", "calc_thresholds", "(", "rbh", ",", "'rbh.scores.summary.txt'", ",", "thresholds", ")", "# print rbh score summary to rbh_score_summary.txt and", "# calculate normalized bit score cutoff for each pair of", "# genomes, if desired", "g", "=", "rbh_network", "(", "id2desc", ",", "rbh", ",", "file_name", "=", "'rbh.network.edges.txt'", ")", "filtered_g", ",", "filtered_rbh", "=", "rbh_network", "(", "id2desc", ",", "rbh", ",", "'rbh.filtered.network.edges.txt'", ",", "thresholds", ")", "calc_thresholds", "(", "filtered_rbh", ",", "file_name", "=", "'rbh.filtered.scores.summary.txt'", ")", "print_summary", "(", "filtered_g", ",", "fastas", ",", "id2desc", ",", "file_name", "=", "'rbh.filtered.network.nodes.txt'", ")", "print_network_matrix", "(", "filtered_g", ",", "fastas", ",", "id2desc", ",", "file_name", "=", "'rbh.filtered.network.matrix.txt'", ")", "print_genome_matrix", "(", "filtered_rbh", ",", "fastas", ",", "id2desc", ",", "file_name", "=", "'rbh.filtered.network.genome_matrix.txt'", ")", "split_g", "=", "split_network", "(", "filtered_g", ",", "id2desc", ",", "file_name", "=", "'rbh.filtered.split.network.edges.txt'", ")", "print_summary", "(", "split_g", ",", "fastas", ",", "id2desc", ",", "file_name", "=", "'rbh.filtered.split.network.nodes.txt'", ")", "print_network_matrix", "(", "split_g", ",", "fastas", ",", "id2desc", ",", "file_name", "=", "'rbh.filtered.split.network.matrix.txt'", ")", "return", "split_g" ]
make and split a rbh network
[ "make", "and", "split", "a", "rbh", "network" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/neto.py#L416-L445
train
consbio/gis-metadata-parser
gis_metadata/iso_metadata_parser.py
IsoParser._parse_raster_info
def _parse_raster_info(self, prop=RASTER_INFO): """ Collapses multiple dimensions into a single raster_info complex struct """ raster_info = {}.fromkeys(_iso_definitions[prop], u'') # Ensure conversion of lists to newlines is in place raster_info['dimensions'] = get_default_for_complex_sub( prop=prop, subprop='dimensions', value=parse_property(self._xml_tree, None, self._data_map, '_ri_num_dims'), xpath=self._data_map['_ri_num_dims'] ) xpath_root = self._get_xroot_for(prop) xpath_map = self._data_structures[prop] for dimension in parse_complex_list(self._xml_tree, xpath_root, xpath_map, RASTER_DIMS): dimension_type = dimension['type'].lower() if dimension_type == 'vertical': raster_info['vertical_count'] = dimension['size'] elif dimension_type == 'column': raster_info['column_count'] = dimension['size'] raster_info['x_resolution'] = u' '.join(dimension[k] for k in ['value', 'units']).strip() elif dimension_type == 'row': raster_info['row_count'] = dimension['size'] raster_info['y_resolution'] = u' '.join(dimension[k] for k in ['value', 'units']).strip() return raster_info if any(raster_info[k] for k in raster_info) else {}
python
def _parse_raster_info(self, prop=RASTER_INFO): """ Collapses multiple dimensions into a single raster_info complex struct """ raster_info = {}.fromkeys(_iso_definitions[prop], u'') # Ensure conversion of lists to newlines is in place raster_info['dimensions'] = get_default_for_complex_sub( prop=prop, subprop='dimensions', value=parse_property(self._xml_tree, None, self._data_map, '_ri_num_dims'), xpath=self._data_map['_ri_num_dims'] ) xpath_root = self._get_xroot_for(prop) xpath_map = self._data_structures[prop] for dimension in parse_complex_list(self._xml_tree, xpath_root, xpath_map, RASTER_DIMS): dimension_type = dimension['type'].lower() if dimension_type == 'vertical': raster_info['vertical_count'] = dimension['size'] elif dimension_type == 'column': raster_info['column_count'] = dimension['size'] raster_info['x_resolution'] = u' '.join(dimension[k] for k in ['value', 'units']).strip() elif dimension_type == 'row': raster_info['row_count'] = dimension['size'] raster_info['y_resolution'] = u' '.join(dimension[k] for k in ['value', 'units']).strip() return raster_info if any(raster_info[k] for k in raster_info) else {}
[ "def", "_parse_raster_info", "(", "self", ",", "prop", "=", "RASTER_INFO", ")", ":", "raster_info", "=", "{", "}", ".", "fromkeys", "(", "_iso_definitions", "[", "prop", "]", ",", "u''", ")", "# Ensure conversion of lists to newlines is in place", "raster_info", "[", "'dimensions'", "]", "=", "get_default_for_complex_sub", "(", "prop", "=", "prop", ",", "subprop", "=", "'dimensions'", ",", "value", "=", "parse_property", "(", "self", ".", "_xml_tree", ",", "None", ",", "self", ".", "_data_map", ",", "'_ri_num_dims'", ")", ",", "xpath", "=", "self", ".", "_data_map", "[", "'_ri_num_dims'", "]", ")", "xpath_root", "=", "self", ".", "_get_xroot_for", "(", "prop", ")", "xpath_map", "=", "self", ".", "_data_structures", "[", "prop", "]", "for", "dimension", "in", "parse_complex_list", "(", "self", ".", "_xml_tree", ",", "xpath_root", ",", "xpath_map", ",", "RASTER_DIMS", ")", ":", "dimension_type", "=", "dimension", "[", "'type'", "]", ".", "lower", "(", ")", "if", "dimension_type", "==", "'vertical'", ":", "raster_info", "[", "'vertical_count'", "]", "=", "dimension", "[", "'size'", "]", "elif", "dimension_type", "==", "'column'", ":", "raster_info", "[", "'column_count'", "]", "=", "dimension", "[", "'size'", "]", "raster_info", "[", "'x_resolution'", "]", "=", "u' '", ".", "join", "(", "dimension", "[", "k", "]", "for", "k", "in", "[", "'value'", ",", "'units'", "]", ")", ".", "strip", "(", ")", "elif", "dimension_type", "==", "'row'", ":", "raster_info", "[", "'row_count'", "]", "=", "dimension", "[", "'size'", "]", "raster_info", "[", "'y_resolution'", "]", "=", "u' '", ".", "join", "(", "dimension", "[", "k", "]", "for", "k", "in", "[", "'value'", ",", "'units'", "]", ")", ".", "strip", "(", ")", "return", "raster_info", "if", "any", "(", "raster_info", "[", "k", "]", "for", "k", "in", "raster_info", ")", "else", "{", "}" ]
Collapses multiple dimensions into a single raster_info complex struct
[ "Collapses", "multiple", "dimensions", "into", "a", "single", "raster_info", "complex", "struct" ]
59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L472-L502
train
consbio/gis-metadata-parser
gis_metadata/iso_metadata_parser.py
IsoParser._update_raster_info
def _update_raster_info(self, **update_props): """ Derives multiple dimensions from a single raster_info complex struct """ tree_to_update = update_props['tree_to_update'] prop = update_props['prop'] values = update_props.pop('values') # Update number of dimensions at raster_info root (applies to all dimensions below) xroot, xpath = None, self._data_map['_ri_num_dims'] raster_info = [update_property(tree_to_update, xroot, xpath, prop, values.get('dimensions', u''))] # Derive vertical, longitude, and latitude dimensions from raster_info xpath_root = self._get_xroot_for(prop) xpath_map = self._data_structures[prop] v_dimension = {} if values.get('vertical_count'): v_dimension = v_dimension.fromkeys(xpath_map, u'') v_dimension['type'] = 'vertical' v_dimension['size'] = values.get('vertical_count', u'') x_dimension = {} if values.get('column_count') or values.get('x_resolution'): x_dimension = x_dimension.fromkeys(xpath_map, u'') x_dimension['type'] = 'column' x_dimension['size'] = values.get('column_count', u'') x_dimension['value'] = values.get('x_resolution', u'') y_dimension = {} if values.get('row_count') or values.get('y_resolution'): y_dimension = y_dimension.fromkeys(xpath_map, u'') y_dimension['type'] = 'row' y_dimension['size'] = values.get('row_count', u'') y_dimension['value'] = values.get('y_resolution', u'') # Update derived dimensions as complex list, and append affected elements for return update_props['prop'] = RASTER_DIMS update_props['values'] = [v_dimension, x_dimension, y_dimension] raster_info += update_complex_list(xpath_root=xpath_root, xpath_map=xpath_map, **update_props) return raster_info
python
def _update_raster_info(self, **update_props): """ Derives multiple dimensions from a single raster_info complex struct """ tree_to_update = update_props['tree_to_update'] prop = update_props['prop'] values = update_props.pop('values') # Update number of dimensions at raster_info root (applies to all dimensions below) xroot, xpath = None, self._data_map['_ri_num_dims'] raster_info = [update_property(tree_to_update, xroot, xpath, prop, values.get('dimensions', u''))] # Derive vertical, longitude, and latitude dimensions from raster_info xpath_root = self._get_xroot_for(prop) xpath_map = self._data_structures[prop] v_dimension = {} if values.get('vertical_count'): v_dimension = v_dimension.fromkeys(xpath_map, u'') v_dimension['type'] = 'vertical' v_dimension['size'] = values.get('vertical_count', u'') x_dimension = {} if values.get('column_count') or values.get('x_resolution'): x_dimension = x_dimension.fromkeys(xpath_map, u'') x_dimension['type'] = 'column' x_dimension['size'] = values.get('column_count', u'') x_dimension['value'] = values.get('x_resolution', u'') y_dimension = {} if values.get('row_count') or values.get('y_resolution'): y_dimension = y_dimension.fromkeys(xpath_map, u'') y_dimension['type'] = 'row' y_dimension['size'] = values.get('row_count', u'') y_dimension['value'] = values.get('y_resolution', u'') # Update derived dimensions as complex list, and append affected elements for return update_props['prop'] = RASTER_DIMS update_props['values'] = [v_dimension, x_dimension, y_dimension] raster_info += update_complex_list(xpath_root=xpath_root, xpath_map=xpath_map, **update_props) return raster_info
[ "def", "_update_raster_info", "(", "self", ",", "*", "*", "update_props", ")", ":", "tree_to_update", "=", "update_props", "[", "'tree_to_update'", "]", "prop", "=", "update_props", "[", "'prop'", "]", "values", "=", "update_props", ".", "pop", "(", "'values'", ")", "# Update number of dimensions at raster_info root (applies to all dimensions below)", "xroot", ",", "xpath", "=", "None", ",", "self", ".", "_data_map", "[", "'_ri_num_dims'", "]", "raster_info", "=", "[", "update_property", "(", "tree_to_update", ",", "xroot", ",", "xpath", ",", "prop", ",", "values", ".", "get", "(", "'dimensions'", ",", "u''", ")", ")", "]", "# Derive vertical, longitude, and latitude dimensions from raster_info", "xpath_root", "=", "self", ".", "_get_xroot_for", "(", "prop", ")", "xpath_map", "=", "self", ".", "_data_structures", "[", "prop", "]", "v_dimension", "=", "{", "}", "if", "values", ".", "get", "(", "'vertical_count'", ")", ":", "v_dimension", "=", "v_dimension", ".", "fromkeys", "(", "xpath_map", ",", "u''", ")", "v_dimension", "[", "'type'", "]", "=", "'vertical'", "v_dimension", "[", "'size'", "]", "=", "values", ".", "get", "(", "'vertical_count'", ",", "u''", ")", "x_dimension", "=", "{", "}", "if", "values", ".", "get", "(", "'column_count'", ")", "or", "values", ".", "get", "(", "'x_resolution'", ")", ":", "x_dimension", "=", "x_dimension", ".", "fromkeys", "(", "xpath_map", ",", "u''", ")", "x_dimension", "[", "'type'", "]", "=", "'column'", "x_dimension", "[", "'size'", "]", "=", "values", ".", "get", "(", "'column_count'", ",", "u''", ")", "x_dimension", "[", "'value'", "]", "=", "values", ".", "get", "(", "'x_resolution'", ",", "u''", ")", "y_dimension", "=", "{", "}", "if", "values", ".", "get", "(", "'row_count'", ")", "or", "values", ".", "get", "(", "'y_resolution'", ")", ":", "y_dimension", "=", "y_dimension", ".", "fromkeys", "(", "xpath_map", ",", "u''", ")", "y_dimension", "[", "'type'", "]", "=", "'row'", "y_dimension", "[", "'size'", "]", "=", "values", ".", "get", "(", "'row_count'", ",", "u''", ")", "y_dimension", "[", "'value'", "]", "=", "values", ".", "get", "(", "'y_resolution'", ",", "u''", ")", "# Update derived dimensions as complex list, and append affected elements for return", "update_props", "[", "'prop'", "]", "=", "RASTER_DIMS", "update_props", "[", "'values'", "]", "=", "[", "v_dimension", ",", "x_dimension", ",", "y_dimension", "]", "raster_info", "+=", "update_complex_list", "(", "xpath_root", "=", "xpath_root", ",", "xpath_map", "=", "xpath_map", ",", "*", "*", "update_props", ")", "return", "raster_info" ]
Derives multiple dimensions from a single raster_info complex struct
[ "Derives", "multiple", "dimensions", "from", "a", "single", "raster_info", "complex", "struct" ]
59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L622-L666
train
consbio/gis-metadata-parser
gis_metadata/iso_metadata_parser.py
IsoParser._trim_xpath
def _trim_xpath(self, xpath, prop): """ Removes primitive type tags from an XPATH """ xroot = self._get_xroot_for(prop) if xroot is None and isinstance(xpath, string_types): xtags = xpath.split(XPATH_DELIM) if xtags[-1] in _iso_tag_primitives: xroot = XPATH_DELIM.join(xtags[:-1]) return xroot
python
def _trim_xpath(self, xpath, prop): """ Removes primitive type tags from an XPATH """ xroot = self._get_xroot_for(prop) if xroot is None and isinstance(xpath, string_types): xtags = xpath.split(XPATH_DELIM) if xtags[-1] in _iso_tag_primitives: xroot = XPATH_DELIM.join(xtags[:-1]) return xroot
[ "def", "_trim_xpath", "(", "self", ",", "xpath", ",", "prop", ")", ":", "xroot", "=", "self", ".", "_get_xroot_for", "(", "prop", ")", "if", "xroot", "is", "None", "and", "isinstance", "(", "xpath", ",", "string_types", ")", ":", "xtags", "=", "xpath", ".", "split", "(", "XPATH_DELIM", ")", "if", "xtags", "[", "-", "1", "]", "in", "_iso_tag_primitives", ":", "xroot", "=", "XPATH_DELIM", ".", "join", "(", "xtags", "[", ":", "-", "1", "]", ")", "return", "xroot" ]
Removes primitive type tags from an XPATH
[ "Removes", "primitive", "type", "tags", "from", "an", "XPATH" ]
59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/iso_metadata_parser.py#L691-L702
train
scottrice/pysteam
pysteam/shortcuts.py
shortcut_app_id
def shortcut_app_id(shortcut): """ Generates the app id for a given shortcut. Steam uses app ids as a unique identifier for games, but since shortcuts dont have a canonical serverside representation they need to be generated on the fly. The important part about this function is that it will generate the same app id as Steam does for a given shortcut """ algorithm = Crc(width = 32, poly = 0x04C11DB7, reflect_in = True, xor_in = 0xffffffff, reflect_out = True, xor_out = 0xffffffff) crc_input = ''.join([shortcut.exe,shortcut.name]) high_32 = algorithm.bit_by_bit(crc_input) | 0x80000000 full_64 = (high_32 << 32) | 0x02000000 return str(full_64)
python
def shortcut_app_id(shortcut): """ Generates the app id for a given shortcut. Steam uses app ids as a unique identifier for games, but since shortcuts dont have a canonical serverside representation they need to be generated on the fly. The important part about this function is that it will generate the same app id as Steam does for a given shortcut """ algorithm = Crc(width = 32, poly = 0x04C11DB7, reflect_in = True, xor_in = 0xffffffff, reflect_out = True, xor_out = 0xffffffff) crc_input = ''.join([shortcut.exe,shortcut.name]) high_32 = algorithm.bit_by_bit(crc_input) | 0x80000000 full_64 = (high_32 << 32) | 0x02000000 return str(full_64)
[ "def", "shortcut_app_id", "(", "shortcut", ")", ":", "algorithm", "=", "Crc", "(", "width", "=", "32", ",", "poly", "=", "0x04C11DB7", ",", "reflect_in", "=", "True", ",", "xor_in", "=", "0xffffffff", ",", "reflect_out", "=", "True", ",", "xor_out", "=", "0xffffffff", ")", "crc_input", "=", "''", ".", "join", "(", "[", "shortcut", ".", "exe", ",", "shortcut", ".", "name", "]", ")", "high_32", "=", "algorithm", ".", "bit_by_bit", "(", "crc_input", ")", "|", "0x80000000", "full_64", "=", "(", "high_32", "<<", "32", ")", "|", "0x02000000", "return", "str", "(", "full_64", ")" ]
Generates the app id for a given shortcut. Steam uses app ids as a unique identifier for games, but since shortcuts dont have a canonical serverside representation they need to be generated on the fly. The important part about this function is that it will generate the same app id as Steam does for a given shortcut
[ "Generates", "the", "app", "id", "for", "a", "given", "shortcut", ".", "Steam", "uses", "app", "ids", "as", "a", "unique", "identifier", "for", "games", "but", "since", "shortcuts", "dont", "have", "a", "canonical", "serverside", "representation", "they", "need", "to", "be", "generated", "on", "the", "fly", ".", "The", "important", "part", "about", "this", "function", "is", "that", "it", "will", "generate", "the", "same", "app", "id", "as", "Steam", "does", "for", "a", "given", "shortcut" ]
1eb2254b5235a053a953e596fa7602d0b110245d
https://github.com/scottrice/pysteam/blob/1eb2254b5235a053a953e596fa7602d0b110245d/pysteam/shortcuts.py#L9-L21
train
mkouhei/bootstrap-py
bootstrap_py/vcs.py
VCS._config
def _config(self): """Execute git config.""" cfg_wr = self.repo.config_writer() cfg_wr.add_section('user') cfg_wr.set_value('user', 'name', self.metadata.author) cfg_wr.set_value('user', 'email', self.metadata.email) cfg_wr.release()
python
def _config(self): """Execute git config.""" cfg_wr = self.repo.config_writer() cfg_wr.add_section('user') cfg_wr.set_value('user', 'name', self.metadata.author) cfg_wr.set_value('user', 'email', self.metadata.email) cfg_wr.release()
[ "def", "_config", "(", "self", ")", ":", "cfg_wr", "=", "self", ".", "repo", ".", "config_writer", "(", ")", "cfg_wr", ".", "add_section", "(", "'user'", ")", "cfg_wr", ".", "set_value", "(", "'user'", ",", "'name'", ",", "self", ".", "metadata", ".", "author", ")", "cfg_wr", ".", "set_value", "(", "'user'", ",", "'email'", ",", "self", ".", "metadata", ".", "email", ")", "cfg_wr", ".", "release", "(", ")" ]
Execute git config.
[ "Execute", "git", "config", "." ]
95d56ed98ef409fd9f019dc352fd1c3711533275
https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/vcs.py#L35-L41
train
mkouhei/bootstrap-py
bootstrap_py/vcs.py
VCS._remote_add
def _remote_add(self): """Execute git remote add.""" self.repo.create_remote( 'origin', '[email protected]:{username}/{repo}.git'.format( username=self.metadata.username, repo=self.metadata.name))
python
def _remote_add(self): """Execute git remote add.""" self.repo.create_remote( 'origin', '[email protected]:{username}/{repo}.git'.format( username=self.metadata.username, repo=self.metadata.name))
[ "def", "_remote_add", "(", "self", ")", ":", "self", ".", "repo", ".", "create_remote", "(", "'origin'", ",", "'[email protected]:{username}/{repo}.git'", ".", "format", "(", "username", "=", "self", ".", "metadata", ".", "username", ",", "repo", "=", "self", ".", "metadata", ".", "name", ")", ")" ]
Execute git remote add.
[ "Execute", "git", "remote", "add", "." ]
95d56ed98ef409fd9f019dc352fd1c3711533275
https://github.com/mkouhei/bootstrap-py/blob/95d56ed98ef409fd9f019dc352fd1c3711533275/bootstrap_py/vcs.py#L47-L53
train
deep-compute/basescript
basescript/basescript.py
BaseScript.start
def start(self): ''' Starts execution of the script ''' # invoke the appropriate sub-command as requested from command-line try: self.args.func() except SystemExit as e: if e.code != 0: raise except KeyboardInterrupt: self.log.warning("exited via keyboard interrupt") except: self.log.exception("exited start function") # set exit code so we know it did not end successfully # TODO different exit codes based on signals ? finally: self._flush_metrics_q.put(None, block=True) self._flush_metrics_q.put(None, block=True, timeout=1) self.log.debug("exited_successfully")
python
def start(self): ''' Starts execution of the script ''' # invoke the appropriate sub-command as requested from command-line try: self.args.func() except SystemExit as e: if e.code != 0: raise except KeyboardInterrupt: self.log.warning("exited via keyboard interrupt") except: self.log.exception("exited start function") # set exit code so we know it did not end successfully # TODO different exit codes based on signals ? finally: self._flush_metrics_q.put(None, block=True) self._flush_metrics_q.put(None, block=True, timeout=1) self.log.debug("exited_successfully")
[ "def", "start", "(", "self", ")", ":", "# invoke the appropriate sub-command as requested from command-line", "try", ":", "self", ".", "args", ".", "func", "(", ")", "except", "SystemExit", "as", "e", ":", "if", "e", ".", "code", "!=", "0", ":", "raise", "except", "KeyboardInterrupt", ":", "self", ".", "log", ".", "warning", "(", "\"exited via keyboard interrupt\"", ")", "except", ":", "self", ".", "log", ".", "exception", "(", "\"exited start function\"", ")", "# set exit code so we know it did not end successfully", "# TODO different exit codes based on signals ?", "finally", ":", "self", ".", "_flush_metrics_q", ".", "put", "(", "None", ",", "block", "=", "True", ")", "self", ".", "_flush_metrics_q", ".", "put", "(", "None", ",", "block", "=", "True", ",", "timeout", "=", "1", ")", "self", ".", "log", ".", "debug", "(", "\"exited_successfully\"", ")" ]
Starts execution of the script
[ "Starts", "execution", "of", "the", "script" ]
f7233963c5291530fcb2444a7f45b556e6407b90
https://github.com/deep-compute/basescript/blob/f7233963c5291530fcb2444a7f45b556e6407b90/basescript/basescript.py#L67-L87
train
deep-compute/basescript
basescript/basescript.py
BaseScript.define_baseargs
def define_baseargs(self, parser): ''' Define basic command-line arguments required by the script. @parser is a parser object created using the `argparse` module. returns: None ''' parser.add_argument('--name', default=sys.argv[0], help='Name to identify this instance') parser.add_argument('--log-level', default=None, help='Logging level as picked from the logging module') parser.add_argument('--log-format', default=None, # TODO add more formats choices=("json", "pretty",), help=("Force the format of the logs. By default, if the " "command is from a terminal, print colorful logs. " "Otherwise print json."), ) parser.add_argument('--log-file', default=None, help='Writes logs to log file if specified, default: %(default)s', ) parser.add_argument('--quiet', default=False, action="store_true", help='if true, does not print logs to stderr, default: %(default)s', ) parser.add_argument('--metric-grouping-interval', default=None, type=int, help='To group metrics based on time interval ex:10 i.e;(10 sec)', ) parser.add_argument('--debug', default=False, action="store_true", help='To run the code in debug mode', )
python
def define_baseargs(self, parser): ''' Define basic command-line arguments required by the script. @parser is a parser object created using the `argparse` module. returns: None ''' parser.add_argument('--name', default=sys.argv[0], help='Name to identify this instance') parser.add_argument('--log-level', default=None, help='Logging level as picked from the logging module') parser.add_argument('--log-format', default=None, # TODO add more formats choices=("json", "pretty",), help=("Force the format of the logs. By default, if the " "command is from a terminal, print colorful logs. " "Otherwise print json."), ) parser.add_argument('--log-file', default=None, help='Writes logs to log file if specified, default: %(default)s', ) parser.add_argument('--quiet', default=False, action="store_true", help='if true, does not print logs to stderr, default: %(default)s', ) parser.add_argument('--metric-grouping-interval', default=None, type=int, help='To group metrics based on time interval ex:10 i.e;(10 sec)', ) parser.add_argument('--debug', default=False, action="store_true", help='To run the code in debug mode', )
[ "def", "define_baseargs", "(", "self", ",", "parser", ")", ":", "parser", ".", "add_argument", "(", "'--name'", ",", "default", "=", "sys", ".", "argv", "[", "0", "]", ",", "help", "=", "'Name to identify this instance'", ")", "parser", ".", "add_argument", "(", "'--log-level'", ",", "default", "=", "None", ",", "help", "=", "'Logging level as picked from the logging module'", ")", "parser", ".", "add_argument", "(", "'--log-format'", ",", "default", "=", "None", ",", "# TODO add more formats", "choices", "=", "(", "\"json\"", ",", "\"pretty\"", ",", ")", ",", "help", "=", "(", "\"Force the format of the logs. By default, if the \"", "\"command is from a terminal, print colorful logs. \"", "\"Otherwise print json.\"", ")", ",", ")", "parser", ".", "add_argument", "(", "'--log-file'", ",", "default", "=", "None", ",", "help", "=", "'Writes logs to log file if specified, default: %(default)s'", ",", ")", "parser", ".", "add_argument", "(", "'--quiet'", ",", "default", "=", "False", ",", "action", "=", "\"store_true\"", ",", "help", "=", "'if true, does not print logs to stderr, default: %(default)s'", ",", ")", "parser", ".", "add_argument", "(", "'--metric-grouping-interval'", ",", "default", "=", "None", ",", "type", "=", "int", ",", "help", "=", "'To group metrics based on time interval ex:10 i.e;(10 sec)'", ",", ")", "parser", ".", "add_argument", "(", "'--debug'", ",", "default", "=", "False", ",", "action", "=", "\"store_true\"", ",", "help", "=", "'To run the code in debug mode'", ",", ")" ]
Define basic command-line arguments required by the script. @parser is a parser object created using the `argparse` module. returns: None
[ "Define", "basic", "command", "-", "line", "arguments", "required", "by", "the", "script", "." ]
f7233963c5291530fcb2444a7f45b556e6407b90
https://github.com/deep-compute/basescript/blob/f7233963c5291530fcb2444a7f45b556e6407b90/basescript/basescript.py#L123-L151
train
elbow-jason/Uno-deprecated
uno/parser/source_coder.py
SourceCoder.cleanup_payload
def cleanup_payload(self, payload): """ Basically, turns payload that looks like ' \\n ' to ''. In the calling function, if this function returns '' no object is added for that payload. """ p = payload.replace('\n', '') p = p.rstrip() p = p.lstrip() return p
python
def cleanup_payload(self, payload): """ Basically, turns payload that looks like ' \\n ' to ''. In the calling function, if this function returns '' no object is added for that payload. """ p = payload.replace('\n', '') p = p.rstrip() p = p.lstrip() return p
[ "def", "cleanup_payload", "(", "self", ",", "payload", ")", ":", "p", "=", "payload", ".", "replace", "(", "'\\n'", ",", "''", ")", "p", "=", "p", ".", "rstrip", "(", ")", "p", "=", "p", ".", "lstrip", "(", ")", "return", "p" ]
Basically, turns payload that looks like ' \\n ' to ''. In the calling function, if this function returns '' no object is added for that payload.
[ "Basically", "turns", "payload", "that", "looks", "like", "\\\\", "n", "to", ".", "In", "the", "calling", "function", "if", "this", "function", "returns", "no", "object", "is", "added", "for", "that", "payload", "." ]
4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4
https://github.com/elbow-jason/Uno-deprecated/blob/4ad07d7b84e5b6e3e2b2c89db69448906f24b4e4/uno/parser/source_coder.py#L73-L82
train
consbio/gis-metadata-parser
gis_metadata/utils.py
get_default_for
def get_default_for(prop, value): """ Ensures complex property types have the correct default values """ prop = prop.strip('_') # Handle alternate props (leading underscores) val = reduce_value(value) # Filtering of value happens here if prop in _COMPLEX_LISTS: return wrap_value(val) elif prop in _COMPLEX_STRUCTS: return val or {} else: return u'' if val is None else val
python
def get_default_for(prop, value): """ Ensures complex property types have the correct default values """ prop = prop.strip('_') # Handle alternate props (leading underscores) val = reduce_value(value) # Filtering of value happens here if prop in _COMPLEX_LISTS: return wrap_value(val) elif prop in _COMPLEX_STRUCTS: return val or {} else: return u'' if val is None else val
[ "def", "get_default_for", "(", "prop", ",", "value", ")", ":", "prop", "=", "prop", ".", "strip", "(", "'_'", ")", "# Handle alternate props (leading underscores)", "val", "=", "reduce_value", "(", "value", ")", "# Filtering of value happens here", "if", "prop", "in", "_COMPLEX_LISTS", ":", "return", "wrap_value", "(", "val", ")", "elif", "prop", "in", "_COMPLEX_STRUCTS", ":", "return", "val", "or", "{", "}", "else", ":", "return", "u''", "if", "val", "is", "None", "else", "val" ]
Ensures complex property types have the correct default values
[ "Ensures", "complex", "property", "types", "have", "the", "correct", "default", "values" ]
59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L223-L234
train
consbio/gis-metadata-parser
gis_metadata/utils.py
update_property
def update_property(tree_to_update, xpath_root, xpaths, prop, values, supported=None): """ Either update the tree the default way, or call the custom updater Default Way: Existing values in the tree are overwritten. If xpaths contains a single path, then each value is written to the tree at that path. If xpaths contains a list of xpaths, then the values corresponding to each xpath index are written to their respective locations. In either case, empty values are ignored. :param tree_to_update: the XML tree compatible with element_utils to be updated :param xpath_root: the XPATH location shared by all the xpaths passed in :param xpaths: a string or a list of strings representing the XPATH location(s) to which to write values :param prop: the name of the property of the parser containing the value(s) with which to update the tree :param values: a single value, or a list of values to write to the specified XPATHs :see: ParserProperty for more on custom updaters :return: a list of all elements updated by this operation """ if supported and prop.startswith('_') and prop.strip('_') in supported: values = u'' # Remove alternate elements: write values only to primary location else: values = get_default_for(prop, values) # Enforce defaults as required per property if not xpaths: return [] elif not isinstance(xpaths, ParserProperty): return _update_property(tree_to_update, xpath_root, xpaths, values) else: # Call ParserProperty.set_prop without xpath_root (managed internally) return xpaths.set_prop(tree_to_update=tree_to_update, prop=prop, values=values)
python
def update_property(tree_to_update, xpath_root, xpaths, prop, values, supported=None): """ Either update the tree the default way, or call the custom updater Default Way: Existing values in the tree are overwritten. If xpaths contains a single path, then each value is written to the tree at that path. If xpaths contains a list of xpaths, then the values corresponding to each xpath index are written to their respective locations. In either case, empty values are ignored. :param tree_to_update: the XML tree compatible with element_utils to be updated :param xpath_root: the XPATH location shared by all the xpaths passed in :param xpaths: a string or a list of strings representing the XPATH location(s) to which to write values :param prop: the name of the property of the parser containing the value(s) with which to update the tree :param values: a single value, or a list of values to write to the specified XPATHs :see: ParserProperty for more on custom updaters :return: a list of all elements updated by this operation """ if supported and prop.startswith('_') and prop.strip('_') in supported: values = u'' # Remove alternate elements: write values only to primary location else: values = get_default_for(prop, values) # Enforce defaults as required per property if not xpaths: return [] elif not isinstance(xpaths, ParserProperty): return _update_property(tree_to_update, xpath_root, xpaths, values) else: # Call ParserProperty.set_prop without xpath_root (managed internally) return xpaths.set_prop(tree_to_update=tree_to_update, prop=prop, values=values)
[ "def", "update_property", "(", "tree_to_update", ",", "xpath_root", ",", "xpaths", ",", "prop", ",", "values", ",", "supported", "=", "None", ")", ":", "if", "supported", "and", "prop", ".", "startswith", "(", "'_'", ")", "and", "prop", ".", "strip", "(", "'_'", ")", "in", "supported", ":", "values", "=", "u''", "# Remove alternate elements: write values only to primary location", "else", ":", "values", "=", "get_default_for", "(", "prop", ",", "values", ")", "# Enforce defaults as required per property", "if", "not", "xpaths", ":", "return", "[", "]", "elif", "not", "isinstance", "(", "xpaths", ",", "ParserProperty", ")", ":", "return", "_update_property", "(", "tree_to_update", ",", "xpath_root", ",", "xpaths", ",", "values", ")", "else", ":", "# Call ParserProperty.set_prop without xpath_root (managed internally)", "return", "xpaths", ".", "set_prop", "(", "tree_to_update", "=", "tree_to_update", ",", "prop", "=", "prop", ",", "values", "=", "values", ")" ]
Either update the tree the default way, or call the custom updater Default Way: Existing values in the tree are overwritten. If xpaths contains a single path, then each value is written to the tree at that path. If xpaths contains a list of xpaths, then the values corresponding to each xpath index are written to their respective locations. In either case, empty values are ignored. :param tree_to_update: the XML tree compatible with element_utils to be updated :param xpath_root: the XPATH location shared by all the xpaths passed in :param xpaths: a string or a list of strings representing the XPATH location(s) to which to write values :param prop: the name of the property of the parser containing the value(s) with which to update the tree :param values: a single value, or a list of values to write to the specified XPATHs :see: ParserProperty for more on custom updaters :return: a list of all elements updated by this operation
[ "Either", "update", "the", "tree", "the", "default", "way", "or", "call", "the", "custom", "updater" ]
59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L392-L423
train
consbio/gis-metadata-parser
gis_metadata/utils.py
_update_property
def _update_property(tree_to_update, xpath_root, xpaths, values): """ Default update operation for a single parser property. If xpaths contains one xpath, then one element per value will be inserted at that location in the tree_to_update; otherwise, the number of values must match the number of xpaths. """ # Inner function to update a specific XPATH with the values provided def update_element(elem, idx, root, path, vals): """ Internal helper function to encapsulate single item update """ has_root = bool(root and len(path) > len(root) and path.startswith(root)) path, attr = get_xpath_tuple(path) # 'path/@attr' to ('path', 'attr') if attr: removed = [get_element(elem, path)] remove_element_attributes(removed[0], attr) elif not has_root: removed = wrap_value(remove_element(elem, path)) else: path = get_xpath_branch(root, path) removed = [] if idx != 0 else [remove_element(e, path, True) for e in get_elements(elem, root)] if not vals: return removed items = [] for i, val in enumerate(wrap_value(vals)): elem_to_update = elem if has_root: elem_to_update = insert_element(elem, (i + idx), root) val = val.decode('utf-8') if not isinstance(val, string_types) else val if not attr: items.append(insert_element(elem_to_update, i, path, val)) elif path: items.append(insert_element(elem_to_update, i, path, **{attr: val})) else: set_element_attributes(elem_to_update, **{attr: val}) items.append(elem_to_update) return items # Code to update each of the XPATHs with each of the values xpaths = reduce_value(xpaths) values = filter_empty(values) if isinstance(xpaths, string_types): return update_element(tree_to_update, 0, xpath_root, xpaths, values) else: each = [] for index, xpath in enumerate(xpaths): value = values[index] if values else None each.extend(update_element(tree_to_update, index, xpath_root, xpath, value)) return each
python
def _update_property(tree_to_update, xpath_root, xpaths, values): """ Default update operation for a single parser property. If xpaths contains one xpath, then one element per value will be inserted at that location in the tree_to_update; otherwise, the number of values must match the number of xpaths. """ # Inner function to update a specific XPATH with the values provided def update_element(elem, idx, root, path, vals): """ Internal helper function to encapsulate single item update """ has_root = bool(root and len(path) > len(root) and path.startswith(root)) path, attr = get_xpath_tuple(path) # 'path/@attr' to ('path', 'attr') if attr: removed = [get_element(elem, path)] remove_element_attributes(removed[0], attr) elif not has_root: removed = wrap_value(remove_element(elem, path)) else: path = get_xpath_branch(root, path) removed = [] if idx != 0 else [remove_element(e, path, True) for e in get_elements(elem, root)] if not vals: return removed items = [] for i, val in enumerate(wrap_value(vals)): elem_to_update = elem if has_root: elem_to_update = insert_element(elem, (i + idx), root) val = val.decode('utf-8') if not isinstance(val, string_types) else val if not attr: items.append(insert_element(elem_to_update, i, path, val)) elif path: items.append(insert_element(elem_to_update, i, path, **{attr: val})) else: set_element_attributes(elem_to_update, **{attr: val}) items.append(elem_to_update) return items # Code to update each of the XPATHs with each of the values xpaths = reduce_value(xpaths) values = filter_empty(values) if isinstance(xpaths, string_types): return update_element(tree_to_update, 0, xpath_root, xpaths, values) else: each = [] for index, xpath in enumerate(xpaths): value = values[index] if values else None each.extend(update_element(tree_to_update, index, xpath_root, xpath, value)) return each
[ "def", "_update_property", "(", "tree_to_update", ",", "xpath_root", ",", "xpaths", ",", "values", ")", ":", "# Inner function to update a specific XPATH with the values provided", "def", "update_element", "(", "elem", ",", "idx", ",", "root", ",", "path", ",", "vals", ")", ":", "\"\"\" Internal helper function to encapsulate single item update \"\"\"", "has_root", "=", "bool", "(", "root", "and", "len", "(", "path", ")", ">", "len", "(", "root", ")", "and", "path", ".", "startswith", "(", "root", ")", ")", "path", ",", "attr", "=", "get_xpath_tuple", "(", "path", ")", "# 'path/@attr' to ('path', 'attr')", "if", "attr", ":", "removed", "=", "[", "get_element", "(", "elem", ",", "path", ")", "]", "remove_element_attributes", "(", "removed", "[", "0", "]", ",", "attr", ")", "elif", "not", "has_root", ":", "removed", "=", "wrap_value", "(", "remove_element", "(", "elem", ",", "path", ")", ")", "else", ":", "path", "=", "get_xpath_branch", "(", "root", ",", "path", ")", "removed", "=", "[", "]", "if", "idx", "!=", "0", "else", "[", "remove_element", "(", "e", ",", "path", ",", "True", ")", "for", "e", "in", "get_elements", "(", "elem", ",", "root", ")", "]", "if", "not", "vals", ":", "return", "removed", "items", "=", "[", "]", "for", "i", ",", "val", "in", "enumerate", "(", "wrap_value", "(", "vals", ")", ")", ":", "elem_to_update", "=", "elem", "if", "has_root", ":", "elem_to_update", "=", "insert_element", "(", "elem", ",", "(", "i", "+", "idx", ")", ",", "root", ")", "val", "=", "val", ".", "decode", "(", "'utf-8'", ")", "if", "not", "isinstance", "(", "val", ",", "string_types", ")", "else", "val", "if", "not", "attr", ":", "items", ".", "append", "(", "insert_element", "(", "elem_to_update", ",", "i", ",", "path", ",", "val", ")", ")", "elif", "path", ":", "items", ".", "append", "(", "insert_element", "(", "elem_to_update", ",", "i", ",", "path", ",", "*", "*", "{", "attr", ":", "val", "}", ")", ")", "else", ":", "set_element_attributes", "(", "elem_to_update", ",", "*", "*", "{", "attr", ":", "val", "}", ")", "items", ".", "append", "(", "elem_to_update", ")", "return", "items", "# Code to update each of the XPATHs with each of the values", "xpaths", "=", "reduce_value", "(", "xpaths", ")", "values", "=", "filter_empty", "(", "values", ")", "if", "isinstance", "(", "xpaths", ",", "string_types", ")", ":", "return", "update_element", "(", "tree_to_update", ",", "0", ",", "xpath_root", ",", "xpaths", ",", "values", ")", "else", ":", "each", "=", "[", "]", "for", "index", ",", "xpath", "in", "enumerate", "(", "xpaths", ")", ":", "value", "=", "values", "[", "index", "]", "if", "values", "else", "None", "each", ".", "extend", "(", "update_element", "(", "tree_to_update", ",", "index", ",", "xpath_root", ",", "xpath", ",", "value", ")", ")", "return", "each" ]
Default update operation for a single parser property. If xpaths contains one xpath, then one element per value will be inserted at that location in the tree_to_update; otherwise, the number of values must match the number of xpaths.
[ "Default", "update", "operation", "for", "a", "single", "parser", "property", ".", "If", "xpaths", "contains", "one", "xpath", "then", "one", "element", "per", "value", "will", "be", "inserted", "at", "that", "location", "in", "the", "tree_to_update", ";", "otherwise", "the", "number", "of", "values", "must", "match", "the", "number", "of", "xpaths", "." ]
59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L426-L486
train
consbio/gis-metadata-parser
gis_metadata/utils.py
validate_complex
def validate_complex(prop, value, xpath_map=None): """ Default validation for single complex data structure """ if value is not None: validate_type(prop, value, dict) if prop in _complex_definitions: complex_keys = _complex_definitions[prop] else: complex_keys = {} if xpath_map is None else xpath_map for complex_prop, complex_val in iteritems(value): complex_key = '.'.join((prop, complex_prop)) if complex_prop not in complex_keys: _validation_error(prop, None, value, ('keys: {0}'.format(','.join(complex_keys)))) validate_type(complex_key, complex_val, (string_types, list))
python
def validate_complex(prop, value, xpath_map=None): """ Default validation for single complex data structure """ if value is not None: validate_type(prop, value, dict) if prop in _complex_definitions: complex_keys = _complex_definitions[prop] else: complex_keys = {} if xpath_map is None else xpath_map for complex_prop, complex_val in iteritems(value): complex_key = '.'.join((prop, complex_prop)) if complex_prop not in complex_keys: _validation_error(prop, None, value, ('keys: {0}'.format(','.join(complex_keys)))) validate_type(complex_key, complex_val, (string_types, list))
[ "def", "validate_complex", "(", "prop", ",", "value", ",", "xpath_map", "=", "None", ")", ":", "if", "value", "is", "not", "None", ":", "validate_type", "(", "prop", ",", "value", ",", "dict", ")", "if", "prop", "in", "_complex_definitions", ":", "complex_keys", "=", "_complex_definitions", "[", "prop", "]", "else", ":", "complex_keys", "=", "{", "}", "if", "xpath_map", "is", "None", "else", "xpath_map", "for", "complex_prop", ",", "complex_val", "in", "iteritems", "(", "value", ")", ":", "complex_key", "=", "'.'", ".", "join", "(", "(", "prop", ",", "complex_prop", ")", ")", "if", "complex_prop", "not", "in", "complex_keys", ":", "_validation_error", "(", "prop", ",", "None", ",", "value", ",", "(", "'keys: {0}'", ".", "format", "(", "','", ".", "join", "(", "complex_keys", ")", ")", ")", ")", "validate_type", "(", "complex_key", ",", "complex_val", ",", "(", "string_types", ",", "list", ")", ")" ]
Default validation for single complex data structure
[ "Default", "validation", "for", "single", "complex", "data", "structure" ]
59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L572-L589
train
consbio/gis-metadata-parser
gis_metadata/utils.py
validate_complex_list
def validate_complex_list(prop, value, xpath_map=None): """ Default validation for Attribute Details data structure """ if value is not None: validate_type(prop, value, (dict, list)) if prop in _complex_definitions: complex_keys = _complex_definitions[prop] else: complex_keys = {} if xpath_map is None else xpath_map for idx, complex_struct in enumerate(wrap_value(value)): cs_idx = prop + '[' + str(idx) + ']' validate_type(cs_idx, complex_struct, dict) for cs_prop, cs_val in iteritems(complex_struct): cs_key = '.'.join((cs_idx, cs_prop)) if cs_prop not in complex_keys: _validation_error(prop, None, value, ('keys: {0}'.format(','.join(complex_keys)))) if not isinstance(cs_val, list): validate_type(cs_key, cs_val, (string_types, list)) else: for list_idx, list_val in enumerate(cs_val): list_prop = cs_key + '[' + str(list_idx) + ']' validate_type(list_prop, list_val, string_types)
python
def validate_complex_list(prop, value, xpath_map=None): """ Default validation for Attribute Details data structure """ if value is not None: validate_type(prop, value, (dict, list)) if prop in _complex_definitions: complex_keys = _complex_definitions[prop] else: complex_keys = {} if xpath_map is None else xpath_map for idx, complex_struct in enumerate(wrap_value(value)): cs_idx = prop + '[' + str(idx) + ']' validate_type(cs_idx, complex_struct, dict) for cs_prop, cs_val in iteritems(complex_struct): cs_key = '.'.join((cs_idx, cs_prop)) if cs_prop not in complex_keys: _validation_error(prop, None, value, ('keys: {0}'.format(','.join(complex_keys)))) if not isinstance(cs_val, list): validate_type(cs_key, cs_val, (string_types, list)) else: for list_idx, list_val in enumerate(cs_val): list_prop = cs_key + '[' + str(list_idx) + ']' validate_type(list_prop, list_val, string_types)
[ "def", "validate_complex_list", "(", "prop", ",", "value", ",", "xpath_map", "=", "None", ")", ":", "if", "value", "is", "not", "None", ":", "validate_type", "(", "prop", ",", "value", ",", "(", "dict", ",", "list", ")", ")", "if", "prop", "in", "_complex_definitions", ":", "complex_keys", "=", "_complex_definitions", "[", "prop", "]", "else", ":", "complex_keys", "=", "{", "}", "if", "xpath_map", "is", "None", "else", "xpath_map", "for", "idx", ",", "complex_struct", "in", "enumerate", "(", "wrap_value", "(", "value", ")", ")", ":", "cs_idx", "=", "prop", "+", "'['", "+", "str", "(", "idx", ")", "+", "']'", "validate_type", "(", "cs_idx", ",", "complex_struct", ",", "dict", ")", "for", "cs_prop", ",", "cs_val", "in", "iteritems", "(", "complex_struct", ")", ":", "cs_key", "=", "'.'", ".", "join", "(", "(", "cs_idx", ",", "cs_prop", ")", ")", "if", "cs_prop", "not", "in", "complex_keys", ":", "_validation_error", "(", "prop", ",", "None", ",", "value", ",", "(", "'keys: {0}'", ".", "format", "(", "','", ".", "join", "(", "complex_keys", ")", ")", ")", ")", "if", "not", "isinstance", "(", "cs_val", ",", "list", ")", ":", "validate_type", "(", "cs_key", ",", "cs_val", ",", "(", "string_types", ",", "list", ")", ")", "else", ":", "for", "list_idx", ",", "list_val", "in", "enumerate", "(", "cs_val", ")", ":", "list_prop", "=", "cs_key", "+", "'['", "+", "str", "(", "list_idx", ")", "+", "']'", "validate_type", "(", "list_prop", ",", "list_val", ",", "string_types", ")" ]
Default validation for Attribute Details data structure
[ "Default", "validation", "for", "Attribute", "Details", "data", "structure" ]
59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L592-L618
train
consbio/gis-metadata-parser
gis_metadata/utils.py
validate_dates
def validate_dates(prop, value, xpath_map=None): """ Default validation for Date Types data structure """ if value is not None: validate_type(prop, value, dict) date_keys = set(value) if date_keys: if DATE_TYPE not in date_keys or DATE_VALUES not in date_keys: if prop in _complex_definitions: complex_keys = _complex_definitions[prop] else: complex_keys = _complex_definitions[DATES] if xpath_map is None else xpath_map _validation_error(prop, None, value, ('keys: {0}'.format(','.join(complex_keys)))) date_type = value[DATE_TYPE] if date_type not in DATE_TYPES: _validation_error('dates.type', None, date_type, DATE_TYPES) date_vals = value[DATE_VALUES] validate_type('dates.values', date_vals, list) dates_len = len(date_vals) if date_type == DATE_TYPE_MISSING and dates_len != 0: _validation_error('len(dates.values)', None, dates_len, 0) if date_type == DATE_TYPE_SINGLE and dates_len != 1: _validation_error('len(dates.values)', None, dates_len, 1) if date_type == DATE_TYPE_RANGE and dates_len != 2: _validation_error('len(dates.values)', None, dates_len, 2) if date_type == DATE_TYPE_MULTIPLE and dates_len < 2: _validation_error('len(dates.values)', None, dates_len, 'at least two') for idx, date in enumerate(date_vals): date_key = 'dates.value[' + str(idx) + ']' validate_type(date_key, date, string_types)
python
def validate_dates(prop, value, xpath_map=None): """ Default validation for Date Types data structure """ if value is not None: validate_type(prop, value, dict) date_keys = set(value) if date_keys: if DATE_TYPE not in date_keys or DATE_VALUES not in date_keys: if prop in _complex_definitions: complex_keys = _complex_definitions[prop] else: complex_keys = _complex_definitions[DATES] if xpath_map is None else xpath_map _validation_error(prop, None, value, ('keys: {0}'.format(','.join(complex_keys)))) date_type = value[DATE_TYPE] if date_type not in DATE_TYPES: _validation_error('dates.type', None, date_type, DATE_TYPES) date_vals = value[DATE_VALUES] validate_type('dates.values', date_vals, list) dates_len = len(date_vals) if date_type == DATE_TYPE_MISSING and dates_len != 0: _validation_error('len(dates.values)', None, dates_len, 0) if date_type == DATE_TYPE_SINGLE and dates_len != 1: _validation_error('len(dates.values)', None, dates_len, 1) if date_type == DATE_TYPE_RANGE and dates_len != 2: _validation_error('len(dates.values)', None, dates_len, 2) if date_type == DATE_TYPE_MULTIPLE and dates_len < 2: _validation_error('len(dates.values)', None, dates_len, 'at least two') for idx, date in enumerate(date_vals): date_key = 'dates.value[' + str(idx) + ']' validate_type(date_key, date, string_types)
[ "def", "validate_dates", "(", "prop", ",", "value", ",", "xpath_map", "=", "None", ")", ":", "if", "value", "is", "not", "None", ":", "validate_type", "(", "prop", ",", "value", ",", "dict", ")", "date_keys", "=", "set", "(", "value", ")", "if", "date_keys", ":", "if", "DATE_TYPE", "not", "in", "date_keys", "or", "DATE_VALUES", "not", "in", "date_keys", ":", "if", "prop", "in", "_complex_definitions", ":", "complex_keys", "=", "_complex_definitions", "[", "prop", "]", "else", ":", "complex_keys", "=", "_complex_definitions", "[", "DATES", "]", "if", "xpath_map", "is", "None", "else", "xpath_map", "_validation_error", "(", "prop", ",", "None", ",", "value", ",", "(", "'keys: {0}'", ".", "format", "(", "','", ".", "join", "(", "complex_keys", ")", ")", ")", ")", "date_type", "=", "value", "[", "DATE_TYPE", "]", "if", "date_type", "not", "in", "DATE_TYPES", ":", "_validation_error", "(", "'dates.type'", ",", "None", ",", "date_type", ",", "DATE_TYPES", ")", "date_vals", "=", "value", "[", "DATE_VALUES", "]", "validate_type", "(", "'dates.values'", ",", "date_vals", ",", "list", ")", "dates_len", "=", "len", "(", "date_vals", ")", "if", "date_type", "==", "DATE_TYPE_MISSING", "and", "dates_len", "!=", "0", ":", "_validation_error", "(", "'len(dates.values)'", ",", "None", ",", "dates_len", ",", "0", ")", "if", "date_type", "==", "DATE_TYPE_SINGLE", "and", "dates_len", "!=", "1", ":", "_validation_error", "(", "'len(dates.values)'", ",", "None", ",", "dates_len", ",", "1", ")", "if", "date_type", "==", "DATE_TYPE_RANGE", "and", "dates_len", "!=", "2", ":", "_validation_error", "(", "'len(dates.values)'", ",", "None", ",", "dates_len", ",", "2", ")", "if", "date_type", "==", "DATE_TYPE_MULTIPLE", "and", "dates_len", "<", "2", ":", "_validation_error", "(", "'len(dates.values)'", ",", "None", ",", "dates_len", ",", "'at least two'", ")", "for", "idx", ",", "date", "in", "enumerate", "(", "date_vals", ")", ":", "date_key", "=", "'dates.value['", "+", "str", "(", "idx", ")", "+", "']'", "validate_type", "(", "date_key", ",", "date", ",", "string_types", ")" ]
Default validation for Date Types data structure
[ "Default", "validation", "for", "Date", "Types", "data", "structure" ]
59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L621-L663
train
consbio/gis-metadata-parser
gis_metadata/utils.py
validate_process_steps
def validate_process_steps(prop, value): """ Default validation for Process Steps data structure """ if value is not None: validate_type(prop, value, (dict, list)) procstep_keys = set(_complex_definitions[prop]) for idx, procstep in enumerate(wrap_value(value)): ps_idx = prop + '[' + str(idx) + ']' validate_type(ps_idx, procstep, dict) for ps_prop, ps_val in iteritems(procstep): ps_key = '.'.join((ps_idx, ps_prop)) if ps_prop not in procstep_keys: _validation_error(prop, None, value, ('keys: {0}'.format(','.join(procstep_keys)))) if ps_prop != 'sources': validate_type(ps_key, ps_val, string_types) else: validate_type(ps_key, ps_val, (string_types, list)) for src_idx, src_val in enumerate(wrap_value(ps_val)): src_key = ps_key + '[' + str(src_idx) + ']' validate_type(src_key, src_val, string_types)
python
def validate_process_steps(prop, value): """ Default validation for Process Steps data structure """ if value is not None: validate_type(prop, value, (dict, list)) procstep_keys = set(_complex_definitions[prop]) for idx, procstep in enumerate(wrap_value(value)): ps_idx = prop + '[' + str(idx) + ']' validate_type(ps_idx, procstep, dict) for ps_prop, ps_val in iteritems(procstep): ps_key = '.'.join((ps_idx, ps_prop)) if ps_prop not in procstep_keys: _validation_error(prop, None, value, ('keys: {0}'.format(','.join(procstep_keys)))) if ps_prop != 'sources': validate_type(ps_key, ps_val, string_types) else: validate_type(ps_key, ps_val, (string_types, list)) for src_idx, src_val in enumerate(wrap_value(ps_val)): src_key = ps_key + '[' + str(src_idx) + ']' validate_type(src_key, src_val, string_types)
[ "def", "validate_process_steps", "(", "prop", ",", "value", ")", ":", "if", "value", "is", "not", "None", ":", "validate_type", "(", "prop", ",", "value", ",", "(", "dict", ",", "list", ")", ")", "procstep_keys", "=", "set", "(", "_complex_definitions", "[", "prop", "]", ")", "for", "idx", ",", "procstep", "in", "enumerate", "(", "wrap_value", "(", "value", ")", ")", ":", "ps_idx", "=", "prop", "+", "'['", "+", "str", "(", "idx", ")", "+", "']'", "validate_type", "(", "ps_idx", ",", "procstep", ",", "dict", ")", "for", "ps_prop", ",", "ps_val", "in", "iteritems", "(", "procstep", ")", ":", "ps_key", "=", "'.'", ".", "join", "(", "(", "ps_idx", ",", "ps_prop", ")", ")", "if", "ps_prop", "not", "in", "procstep_keys", ":", "_validation_error", "(", "prop", ",", "None", ",", "value", ",", "(", "'keys: {0}'", ".", "format", "(", "','", ".", "join", "(", "procstep_keys", ")", ")", ")", ")", "if", "ps_prop", "!=", "'sources'", ":", "validate_type", "(", "ps_key", ",", "ps_val", ",", "string_types", ")", "else", ":", "validate_type", "(", "ps_key", ",", "ps_val", ",", "(", "string_types", ",", "list", ")", ")", "for", "src_idx", ",", "src_val", "in", "enumerate", "(", "wrap_value", "(", "ps_val", ")", ")", ":", "src_key", "=", "ps_key", "+", "'['", "+", "str", "(", "src_idx", ")", "+", "']'", "validate_type", "(", "src_key", ",", "src_val", ",", "string_types", ")" ]
Default validation for Process Steps data structure
[ "Default", "validation", "for", "Process", "Steps", "data", "structure" ]
59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L666-L691
train
consbio/gis-metadata-parser
gis_metadata/utils.py
validate_type
def validate_type(prop, value, expected): """ Default validation for all types """ # Validate on expected type(s), but ignore None: defaults handled elsewhere if value is not None and not isinstance(value, expected): _validation_error(prop, type(value).__name__, None, expected)
python
def validate_type(prop, value, expected): """ Default validation for all types """ # Validate on expected type(s), but ignore None: defaults handled elsewhere if value is not None and not isinstance(value, expected): _validation_error(prop, type(value).__name__, None, expected)
[ "def", "validate_type", "(", "prop", ",", "value", ",", "expected", ")", ":", "# Validate on expected type(s), but ignore None: defaults handled elsewhere", "if", "value", "is", "not", "None", "and", "not", "isinstance", "(", "value", ",", "expected", ")", ":", "_validation_error", "(", "prop", ",", "type", "(", "value", ")", ".", "__name__", ",", "None", ",", "expected", ")" ]
Default validation for all types
[ "Default", "validation", "for", "all", "types" ]
59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L710-L715
train
consbio/gis-metadata-parser
gis_metadata/utils.py
_validation_error
def _validation_error(prop, prop_type, prop_value, expected): """ Default validation for updated properties """ if prop_type is None: attrib = 'value' assigned = prop_value else: attrib = 'type' assigned = prop_type raise ValidationError( 'Invalid property {attrib} for {prop}:\n\t{attrib}: {assigned}\n\texpected: {expected}', attrib=attrib, prop=prop, assigned=assigned, expected=expected, invalid={prop: prop_value} if attrib == 'value' else {} )
python
def _validation_error(prop, prop_type, prop_value, expected): """ Default validation for updated properties """ if prop_type is None: attrib = 'value' assigned = prop_value else: attrib = 'type' assigned = prop_type raise ValidationError( 'Invalid property {attrib} for {prop}:\n\t{attrib}: {assigned}\n\texpected: {expected}', attrib=attrib, prop=prop, assigned=assigned, expected=expected, invalid={prop: prop_value} if attrib == 'value' else {} )
[ "def", "_validation_error", "(", "prop", ",", "prop_type", ",", "prop_value", ",", "expected", ")", ":", "if", "prop_type", "is", "None", ":", "attrib", "=", "'value'", "assigned", "=", "prop_value", "else", ":", "attrib", "=", "'type'", "assigned", "=", "prop_type", "raise", "ValidationError", "(", "'Invalid property {attrib} for {prop}:\\n\\t{attrib}: {assigned}\\n\\texpected: {expected}'", ",", "attrib", "=", "attrib", ",", "prop", "=", "prop", ",", "assigned", "=", "assigned", ",", "expected", "=", "expected", ",", "invalid", "=", "{", "prop", ":", "prop_value", "}", "if", "attrib", "==", "'value'", "else", "{", "}", ")" ]
Default validation for updated properties
[ "Default", "validation", "for", "updated", "properties" ]
59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L718-L732
train
consbio/gis-metadata-parser
gis_metadata/utils.py
ParserProperty.get_prop
def get_prop(self, prop): """ Calls the getter with no arguments and returns its value """ if self._parser is None: raise ConfigurationError('Cannot call ParserProperty."get_prop" with no parser configured') return self._parser(prop) if prop else self._parser()
python
def get_prop(self, prop): """ Calls the getter with no arguments and returns its value """ if self._parser is None: raise ConfigurationError('Cannot call ParserProperty."get_prop" with no parser configured') return self._parser(prop) if prop else self._parser()
[ "def", "get_prop", "(", "self", ",", "prop", ")", ":", "if", "self", ".", "_parser", "is", "None", ":", "raise", "ConfigurationError", "(", "'Cannot call ParserProperty.\"get_prop\" with no parser configured'", ")", "return", "self", ".", "_parser", "(", "prop", ")", "if", "prop", "else", "self", ".", "_parser", "(", ")" ]
Calls the getter with no arguments and returns its value
[ "Calls", "the", "getter", "with", "no", "arguments", "and", "returns", "its", "value" ]
59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/utils.py#L765-L771
train
disqus/nydus
nydus/db/backends/memcache.py
can_group_commands
def can_group_commands(command, next_command): """ Returns a boolean representing whether these commands can be grouped together or not. A few things are taken into account for this decision: For ``set`` commands: - Are all arguments other than the key/value the same? For ``delete`` and ``get`` commands: - Are all arguments other than the key the same? """ multi_capable_commands = ('get', 'set', 'delete') if next_command is None: return False name = command.get_name() # TODO: support multi commands if name not in multi_capable_commands: return False if name != next_command.get_name(): return False # if the shared args (key, or key/value) do not match, we cannot group if grouped_args_for_command(command) != grouped_args_for_command(next_command): return False # If the keyword arguments do not much (e.g. key_prefix, or timeout on set) # then we cannot group if command.get_kwargs() != next_command.get_kwargs(): return False return True
python
def can_group_commands(command, next_command): """ Returns a boolean representing whether these commands can be grouped together or not. A few things are taken into account for this decision: For ``set`` commands: - Are all arguments other than the key/value the same? For ``delete`` and ``get`` commands: - Are all arguments other than the key the same? """ multi_capable_commands = ('get', 'set', 'delete') if next_command is None: return False name = command.get_name() # TODO: support multi commands if name not in multi_capable_commands: return False if name != next_command.get_name(): return False # if the shared args (key, or key/value) do not match, we cannot group if grouped_args_for_command(command) != grouped_args_for_command(next_command): return False # If the keyword arguments do not much (e.g. key_prefix, or timeout on set) # then we cannot group if command.get_kwargs() != next_command.get_kwargs(): return False return True
[ "def", "can_group_commands", "(", "command", ",", "next_command", ")", ":", "multi_capable_commands", "=", "(", "'get'", ",", "'set'", ",", "'delete'", ")", "if", "next_command", "is", "None", ":", "return", "False", "name", "=", "command", ".", "get_name", "(", ")", "# TODO: support multi commands", "if", "name", "not", "in", "multi_capable_commands", ":", "return", "False", "if", "name", "!=", "next_command", ".", "get_name", "(", ")", ":", "return", "False", "# if the shared args (key, or key/value) do not match, we cannot group", "if", "grouped_args_for_command", "(", "command", ")", "!=", "grouped_args_for_command", "(", "next_command", ")", ":", "return", "False", "# If the keyword arguments do not much (e.g. key_prefix, or timeout on set)", "# then we cannot group", "if", "command", ".", "get_kwargs", "(", ")", "!=", "next_command", ".", "get_kwargs", "(", ")", ":", "return", "False", "return", "True" ]
Returns a boolean representing whether these commands can be grouped together or not. A few things are taken into account for this decision: For ``set`` commands: - Are all arguments other than the key/value the same? For ``delete`` and ``get`` commands: - Are all arguments other than the key the same?
[ "Returns", "a", "boolean", "representing", "whether", "these", "commands", "can", "be", "grouped", "together", "or", "not", "." ]
9b505840da47a34f758a830c3992fa5dcb7bb7ad
https://github.com/disqus/nydus/blob/9b505840da47a34f758a830c3992fa5dcb7bb7ad/nydus/db/backends/memcache.py#L97-L135
train
christophertbrown/bioscripts
ctbBio/rp16.py
find_databases
def find_databases(databases): """ define ribosomal proteins and location of curated databases """ # 16 ribosomal proteins in their expected order proteins = ['L15', 'L18', 'L6', 'S8', 'L5', 'L24', 'L14', 'S17', 'L16', 'S3', 'L22', 'S19', 'L2', 'L4', 'L3', 'S10'] # curated databases protein_databases = { 'L14': 'rpL14_JGI_MDM.filtered.faa', 'L15': 'rpL15_JGI_MDM.filtered.faa', 'L16': 'rpL16_JGI_MDM.filtered.faa', 'L18': 'rpL18_JGI_MDM.filtered.faa', 'L22': 'rpL22_JGI_MDM.filtered.faa', 'L24': 'rpL24_JGI_MDM.filtered.faa', 'L2': 'rpL2_JGI_MDM.filtered.faa', 'L3': 'rpL3_JGI_MDM.filtered.faa', 'L4': 'rpL4_JGI_MDM.filtered.faa', 'L5': 'rpL5_JGI_MDM.filtered.faa', 'L6': 'rpL6_JGI_MDM.filtered.faa', 'S10': 'rpS10_JGI_MDM.filtered.faa', 'S17': 'rpS17_JGI_MDM.filtered.faa', 'S19': 'rpS19_JGI_MDM.filtered.faa', 'S3': 'rpS3_JGI_MDM.filtered.faa', 'S8': 'rpS8_JGI_MDM.filtered.faa'} protein_databases = {key: '%s/%s' % (databases, database) \ for key, database in list(protein_databases.items())} return proteins, protein_databases
python
def find_databases(databases): """ define ribosomal proteins and location of curated databases """ # 16 ribosomal proteins in their expected order proteins = ['L15', 'L18', 'L6', 'S8', 'L5', 'L24', 'L14', 'S17', 'L16', 'S3', 'L22', 'S19', 'L2', 'L4', 'L3', 'S10'] # curated databases protein_databases = { 'L14': 'rpL14_JGI_MDM.filtered.faa', 'L15': 'rpL15_JGI_MDM.filtered.faa', 'L16': 'rpL16_JGI_MDM.filtered.faa', 'L18': 'rpL18_JGI_MDM.filtered.faa', 'L22': 'rpL22_JGI_MDM.filtered.faa', 'L24': 'rpL24_JGI_MDM.filtered.faa', 'L2': 'rpL2_JGI_MDM.filtered.faa', 'L3': 'rpL3_JGI_MDM.filtered.faa', 'L4': 'rpL4_JGI_MDM.filtered.faa', 'L5': 'rpL5_JGI_MDM.filtered.faa', 'L6': 'rpL6_JGI_MDM.filtered.faa', 'S10': 'rpS10_JGI_MDM.filtered.faa', 'S17': 'rpS17_JGI_MDM.filtered.faa', 'S19': 'rpS19_JGI_MDM.filtered.faa', 'S3': 'rpS3_JGI_MDM.filtered.faa', 'S8': 'rpS8_JGI_MDM.filtered.faa'} protein_databases = {key: '%s/%s' % (databases, database) \ for key, database in list(protein_databases.items())} return proteins, protein_databases
[ "def", "find_databases", "(", "databases", ")", ":", "# 16 ribosomal proteins in their expected order", "proteins", "=", "[", "'L15'", ",", "'L18'", ",", "'L6'", ",", "'S8'", ",", "'L5'", ",", "'L24'", ",", "'L14'", ",", "'S17'", ",", "'L16'", ",", "'S3'", ",", "'L22'", ",", "'S19'", ",", "'L2'", ",", "'L4'", ",", "'L3'", ",", "'S10'", "]", "# curated databases", "protein_databases", "=", "{", "'L14'", ":", "'rpL14_JGI_MDM.filtered.faa'", ",", "'L15'", ":", "'rpL15_JGI_MDM.filtered.faa'", ",", "'L16'", ":", "'rpL16_JGI_MDM.filtered.faa'", ",", "'L18'", ":", "'rpL18_JGI_MDM.filtered.faa'", ",", "'L22'", ":", "'rpL22_JGI_MDM.filtered.faa'", ",", "'L24'", ":", "'rpL24_JGI_MDM.filtered.faa'", ",", "'L2'", ":", "'rpL2_JGI_MDM.filtered.faa'", ",", "'L3'", ":", "'rpL3_JGI_MDM.filtered.faa'", ",", "'L4'", ":", "'rpL4_JGI_MDM.filtered.faa'", ",", "'L5'", ":", "'rpL5_JGI_MDM.filtered.faa'", ",", "'L6'", ":", "'rpL6_JGI_MDM.filtered.faa'", ",", "'S10'", ":", "'rpS10_JGI_MDM.filtered.faa'", ",", "'S17'", ":", "'rpS17_JGI_MDM.filtered.faa'", ",", "'S19'", ":", "'rpS19_JGI_MDM.filtered.faa'", ",", "'S3'", ":", "'rpS3_JGI_MDM.filtered.faa'", ",", "'S8'", ":", "'rpS8_JGI_MDM.filtered.faa'", "}", "protein_databases", "=", "{", "key", ":", "'%s/%s'", "%", "(", "databases", ",", "database", ")", "for", "key", ",", "database", "in", "list", "(", "protein_databases", ".", "items", "(", ")", ")", "}", "return", "proteins", ",", "protein_databases" ]
define ribosomal proteins and location of curated databases
[ "define", "ribosomal", "proteins", "and", "location", "of", "curated", "databases" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rp16.py#L21-L48
train
christophertbrown/bioscripts
ctbBio/rp16.py
find_next
def find_next(start, stop, i2hits): """ which protein has the best hit, the one to the 'right' or to the 'left?' """ if start not in i2hits and stop in i2hits: index = stop elif stop not in i2hits and start in i2hits: index = start elif start not in i2hits and stop not in i2hits: index = choice([start, stop]) i2hits[index] = [[False]] else: A, B = i2hits[start][0], i2hits[stop][0] if B[10] <= A[10]: index = stop else: index = start if index == start: nstart = start - 1 nstop = stop else: nstop = stop + 1 nstart = start match = i2hits[index][0] rp = match[-1] return index, nstart, nstop, rp, match
python
def find_next(start, stop, i2hits): """ which protein has the best hit, the one to the 'right' or to the 'left?' """ if start not in i2hits and stop in i2hits: index = stop elif stop not in i2hits and start in i2hits: index = start elif start not in i2hits and stop not in i2hits: index = choice([start, stop]) i2hits[index] = [[False]] else: A, B = i2hits[start][0], i2hits[stop][0] if B[10] <= A[10]: index = stop else: index = start if index == start: nstart = start - 1 nstop = stop else: nstop = stop + 1 nstart = start match = i2hits[index][0] rp = match[-1] return index, nstart, nstop, rp, match
[ "def", "find_next", "(", "start", ",", "stop", ",", "i2hits", ")", ":", "if", "start", "not", "in", "i2hits", "and", "stop", "in", "i2hits", ":", "index", "=", "stop", "elif", "stop", "not", "in", "i2hits", "and", "start", "in", "i2hits", ":", "index", "=", "start", "elif", "start", "not", "in", "i2hits", "and", "stop", "not", "in", "i2hits", ":", "index", "=", "choice", "(", "[", "start", ",", "stop", "]", ")", "i2hits", "[", "index", "]", "=", "[", "[", "False", "]", "]", "else", ":", "A", ",", "B", "=", "i2hits", "[", "start", "]", "[", "0", "]", ",", "i2hits", "[", "stop", "]", "[", "0", "]", "if", "B", "[", "10", "]", "<=", "A", "[", "10", "]", ":", "index", "=", "stop", "else", ":", "index", "=", "start", "if", "index", "==", "start", ":", "nstart", "=", "start", "-", "1", "nstop", "=", "stop", "else", ":", "nstop", "=", "stop", "+", "1", "nstart", "=", "start", "match", "=", "i2hits", "[", "index", "]", "[", "0", "]", "rp", "=", "match", "[", "-", "1", "]", "return", "index", ",", "nstart", ",", "nstop", ",", "rp", ",", "match" ]
which protein has the best hit, the one to the 'right' or to the 'left?'
[ "which", "protein", "has", "the", "best", "hit", "the", "one", "to", "the", "right", "or", "to", "the", "left?" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rp16.py#L77-L102
train
christophertbrown/bioscripts
ctbBio/rp16.py
find_ribosomal
def find_ribosomal(rps, scaffolds, s2rp, min_hits, max_hits_rp, max_errors): """ determine which hits represent real ribosomal proteins, identify each in syntenic block max_hits_rp = maximum number of hits to consider per ribosomal protein per scaffold """ for scaffold, proteins in list(s2rp.items()): # for each scaffold, get best hits for each rp hits = {p: [i for i in sorted(hits, key = itemgetter(10))][0:max_hits_rp] for p, hits in list(proteins.items()) if len(hits) > 0} # skip if fewer than min_hits RPs are identified if len(hits) < min_hits: continue best = sorted([hit[0] + [p] for p, hit in list(hits.items())], key = itemgetter(10))[0] block = find_block(rps, scaffolds[scaffold], hits, best, max_errors) if (len(block) - 1) >= min_hits: yield scaffold, block
python
def find_ribosomal(rps, scaffolds, s2rp, min_hits, max_hits_rp, max_errors): """ determine which hits represent real ribosomal proteins, identify each in syntenic block max_hits_rp = maximum number of hits to consider per ribosomal protein per scaffold """ for scaffold, proteins in list(s2rp.items()): # for each scaffold, get best hits for each rp hits = {p: [i for i in sorted(hits, key = itemgetter(10))][0:max_hits_rp] for p, hits in list(proteins.items()) if len(hits) > 0} # skip if fewer than min_hits RPs are identified if len(hits) < min_hits: continue best = sorted([hit[0] + [p] for p, hit in list(hits.items())], key = itemgetter(10))[0] block = find_block(rps, scaffolds[scaffold], hits, best, max_errors) if (len(block) - 1) >= min_hits: yield scaffold, block
[ "def", "find_ribosomal", "(", "rps", ",", "scaffolds", ",", "s2rp", ",", "min_hits", ",", "max_hits_rp", ",", "max_errors", ")", ":", "for", "scaffold", ",", "proteins", "in", "list", "(", "s2rp", ".", "items", "(", ")", ")", ":", "# for each scaffold, get best hits for each rp", "hits", "=", "{", "p", ":", "[", "i", "for", "i", "in", "sorted", "(", "hits", ",", "key", "=", "itemgetter", "(", "10", ")", ")", "]", "[", "0", ":", "max_hits_rp", "]", "for", "p", ",", "hits", "in", "list", "(", "proteins", ".", "items", "(", ")", ")", "if", "len", "(", "hits", ")", ">", "0", "}", "# skip if fewer than min_hits RPs are identified", "if", "len", "(", "hits", ")", "<", "min_hits", ":", "continue", "best", "=", "sorted", "(", "[", "hit", "[", "0", "]", "+", "[", "p", "]", "for", "p", ",", "hit", "in", "list", "(", "hits", ".", "items", "(", ")", ")", "]", ",", "key", "=", "itemgetter", "(", "10", ")", ")", "[", "0", "]", "block", "=", "find_block", "(", "rps", ",", "scaffolds", "[", "scaffold", "]", ",", "hits", ",", "best", ",", "max_errors", ")", "if", "(", "len", "(", "block", ")", "-", "1", ")", ">=", "min_hits", ":", "yield", "scaffold", ",", "block" ]
determine which hits represent real ribosomal proteins, identify each in syntenic block max_hits_rp = maximum number of hits to consider per ribosomal protein per scaffold
[ "determine", "which", "hits", "represent", "real", "ribosomal", "proteins", "identify", "each", "in", "syntenic", "block", "max_hits_rp", "=", "maximum", "number", "of", "hits", "to", "consider", "per", "ribosomal", "protein", "per", "scaffold" ]
83b2566b3a5745437ec651cd6cafddd056846240
https://github.com/christophertbrown/bioscripts/blob/83b2566b3a5745437ec651cd6cafddd056846240/ctbBio/rp16.py#L134-L150
train
smdabdoub/phylotoast
bin/filter_rep_set.py
filter_rep_set
def filter_rep_set(inF, otuSet): """ Parse the rep set file and remove all sequences not associated with unique OTUs. :@type inF: file :@param inF: The representative sequence set :@rtype: list :@return: The set of sequences associated with unique OTUs """ seqs = [] for record in SeqIO.parse(inF, "fasta"): if record.id in otuSet: seqs.append(record) return seqs
python
def filter_rep_set(inF, otuSet): """ Parse the rep set file and remove all sequences not associated with unique OTUs. :@type inF: file :@param inF: The representative sequence set :@rtype: list :@return: The set of sequences associated with unique OTUs """ seqs = [] for record in SeqIO.parse(inF, "fasta"): if record.id in otuSet: seqs.append(record) return seqs
[ "def", "filter_rep_set", "(", "inF", ",", "otuSet", ")", ":", "seqs", "=", "[", "]", "for", "record", "in", "SeqIO", ".", "parse", "(", "inF", ",", "\"fasta\"", ")", ":", "if", "record", ".", "id", "in", "otuSet", ":", "seqs", ".", "append", "(", "record", ")", "return", "seqs" ]
Parse the rep set file and remove all sequences not associated with unique OTUs. :@type inF: file :@param inF: The representative sequence set :@rtype: list :@return: The set of sequences associated with unique OTUs
[ "Parse", "the", "rep", "set", "file", "and", "remove", "all", "sequences", "not", "associated", "with", "unique", "OTUs", "." ]
0b74ef171e6a84761710548501dfac71285a58a3
https://github.com/smdabdoub/phylotoast/blob/0b74ef171e6a84761710548501dfac71285a58a3/bin/filter_rep_set.py#L32-L47
train
consbio/gis-metadata-parser
gis_metadata/arcgis_metadata_parser.py
ArcGISParser._update_report_item
def _update_report_item(self, **update_props): """ Update the text for each element at the configured path if attribute matches """ tree_to_update = update_props['tree_to_update'] prop = update_props['prop'] values = wrap_value(update_props['values']) xroot = self._get_xroot_for(prop) attr_key = 'type' attr_val = u'' if prop == 'attribute_accuracy': attr_val = 'DQQuanAttAcc' elif prop == 'dataset_completeness': attr_val = 'DQCompOm' # Clear (make empty) all elements of the appropriate type for elem in get_elements(tree_to_update, xroot): if get_element_attributes(elem).get(attr_key) == attr_val: clear_element(elem) # Remove all empty elements, including those previously cleared remove_empty_element(tree_to_update, xroot) # Insert elements with correct attributes for each new value attrs = {attr_key: attr_val} updated = [] for idx, value in enumerate(values): elem = insert_element(tree_to_update, idx, xroot, **attrs) updated.append(insert_element(elem, idx, 'measDesc', value)) return updated
python
def _update_report_item(self, **update_props): """ Update the text for each element at the configured path if attribute matches """ tree_to_update = update_props['tree_to_update'] prop = update_props['prop'] values = wrap_value(update_props['values']) xroot = self._get_xroot_for(prop) attr_key = 'type' attr_val = u'' if prop == 'attribute_accuracy': attr_val = 'DQQuanAttAcc' elif prop == 'dataset_completeness': attr_val = 'DQCompOm' # Clear (make empty) all elements of the appropriate type for elem in get_elements(tree_to_update, xroot): if get_element_attributes(elem).get(attr_key) == attr_val: clear_element(elem) # Remove all empty elements, including those previously cleared remove_empty_element(tree_to_update, xroot) # Insert elements with correct attributes for each new value attrs = {attr_key: attr_val} updated = [] for idx, value in enumerate(values): elem = insert_element(tree_to_update, idx, xroot, **attrs) updated.append(insert_element(elem, idx, 'measDesc', value)) return updated
[ "def", "_update_report_item", "(", "self", ",", "*", "*", "update_props", ")", ":", "tree_to_update", "=", "update_props", "[", "'tree_to_update'", "]", "prop", "=", "update_props", "[", "'prop'", "]", "values", "=", "wrap_value", "(", "update_props", "[", "'values'", "]", ")", "xroot", "=", "self", ".", "_get_xroot_for", "(", "prop", ")", "attr_key", "=", "'type'", "attr_val", "=", "u''", "if", "prop", "==", "'attribute_accuracy'", ":", "attr_val", "=", "'DQQuanAttAcc'", "elif", "prop", "==", "'dataset_completeness'", ":", "attr_val", "=", "'DQCompOm'", "# Clear (make empty) all elements of the appropriate type", "for", "elem", "in", "get_elements", "(", "tree_to_update", ",", "xroot", ")", ":", "if", "get_element_attributes", "(", "elem", ")", ".", "get", "(", "attr_key", ")", "==", "attr_val", ":", "clear_element", "(", "elem", ")", "# Remove all empty elements, including those previously cleared", "remove_empty_element", "(", "tree_to_update", ",", "xroot", ")", "# Insert elements with correct attributes for each new value", "attrs", "=", "{", "attr_key", ":", "attr_val", "}", "updated", "=", "[", "]", "for", "idx", ",", "value", "in", "enumerate", "(", "values", ")", ":", "elem", "=", "insert_element", "(", "tree_to_update", ",", "idx", ",", "xroot", ",", "*", "*", "attrs", ")", "updated", ".", "append", "(", "insert_element", "(", "elem", ",", "idx", ",", "'measDesc'", ",", "value", ")", ")", "return", "updated" ]
Update the text for each element at the configured path if attribute matches
[ "Update", "the", "text", "for", "each", "element", "at", "the", "configured", "path", "if", "attribute", "matches" ]
59eefb2e51cd4d8cc3e94623a2167499ca9ef70f
https://github.com/consbio/gis-metadata-parser/blob/59eefb2e51cd4d8cc3e94623a2167499ca9ef70f/gis_metadata/arcgis_metadata_parser.py#L407-L440
train
adafruit/Adafruit_Python_VCNL40xx
Adafruit_VCNL40xx/VCNL40xx.py
VCNL4010._clear_interrupt
def _clear_interrupt(self, intbit): """Clear the specified interrupt bit in the interrupt status register. """ int_status = self._device.readU8(VCNL4010_INTSTAT); int_status &= ~intbit; self._device.write8(VCNL4010_INTSTAT, int_status);
python
def _clear_interrupt(self, intbit): """Clear the specified interrupt bit in the interrupt status register. """ int_status = self._device.readU8(VCNL4010_INTSTAT); int_status &= ~intbit; self._device.write8(VCNL4010_INTSTAT, int_status);
[ "def", "_clear_interrupt", "(", "self", ",", "intbit", ")", ":", "int_status", "=", "self", ".", "_device", ".", "readU8", "(", "VCNL4010_INTSTAT", ")", "int_status", "&=", "~", "intbit", "self", ".", "_device", ".", "write8", "(", "VCNL4010_INTSTAT", ",", "int_status", ")" ]
Clear the specified interrupt bit in the interrupt status register.
[ "Clear", "the", "specified", "interrupt", "bit", "in", "the", "interrupt", "status", "register", "." ]
f88ec755fd23017028b6dec1be0607ff4a018e10
https://github.com/adafruit/Adafruit_Python_VCNL40xx/blob/f88ec755fd23017028b6dec1be0607ff4a018e10/Adafruit_VCNL40xx/VCNL40xx.py#L123-L128
train
skojaku/core-periphery-detection
cpalgorithm/Rombach.py
SimAlg.move
def move(self): """Swaps two nodes""" a = random.randint(0, len(self.state) - 1) b = random.randint(0, len(self.state) - 1) self.state[[a,b]] = self.state[[b,a]]
python
def move(self): """Swaps two nodes""" a = random.randint(0, len(self.state) - 1) b = random.randint(0, len(self.state) - 1) self.state[[a,b]] = self.state[[b,a]]
[ "def", "move", "(", "self", ")", ":", "a", "=", "random", ".", "randint", "(", "0", ",", "len", "(", "self", ".", "state", ")", "-", "1", ")", "b", "=", "random", ".", "randint", "(", "0", ",", "len", "(", "self", ".", "state", ")", "-", "1", ")", "self", ".", "state", "[", "[", "a", ",", "b", "]", "]", "=", "self", ".", "state", "[", "[", "b", ",", "a", "]", "]" ]
Swaps two nodes
[ "Swaps", "two", "nodes" ]
d724e6441066622506ddb54d81ee9a1cfd15f766
https://github.com/skojaku/core-periphery-detection/blob/d724e6441066622506ddb54d81ee9a1cfd15f766/cpalgorithm/Rombach.py#L19-L23
train
wbond/certbuilder
certbuilder/__init__.py
CertificateBuilder.self_signed
def self_signed(self, value): """ A bool - if the certificate should be self-signed. """ self._self_signed = bool(value) if self._self_signed: self._issuer = None
python
def self_signed(self, value): """ A bool - if the certificate should be self-signed. """ self._self_signed = bool(value) if self._self_signed: self._issuer = None
[ "def", "self_signed", "(", "self", ",", "value", ")", ":", "self", ".", "_self_signed", "=", "bool", "(", "value", ")", "if", "self", ".", "_self_signed", ":", "self", ".", "_issuer", "=", "None" ]
A bool - if the certificate should be self-signed.
[ "A", "bool", "-", "if", "the", "certificate", "should", "be", "self", "-", "signed", "." ]
969dae884fa7f73988bbf1dcbec4fb51e234a3c5
https://github.com/wbond/certbuilder/blob/969dae884fa7f73988bbf1dcbec4fb51e234a3c5/certbuilder/__init__.py#L122-L130
train
wbond/certbuilder
certbuilder/__init__.py
CertificateBuilder._get_crl_url
def _get_crl_url(self, distribution_points): """ Grabs the first URL out of a asn1crypto.x509.CRLDistributionPoints object :param distribution_points: The x509.CRLDistributionPoints object to pull the URL out of :return: A unicode string or None """ if distribution_points is None: return None for distribution_point in distribution_points: name = distribution_point['distribution_point'] if name.name == 'full_name' and name.chosen[0].name == 'uniform_resource_identifier': return name.chosen[0].chosen.native return None
python
def _get_crl_url(self, distribution_points): """ Grabs the first URL out of a asn1crypto.x509.CRLDistributionPoints object :param distribution_points: The x509.CRLDistributionPoints object to pull the URL out of :return: A unicode string or None """ if distribution_points is None: return None for distribution_point in distribution_points: name = distribution_point['distribution_point'] if name.name == 'full_name' and name.chosen[0].name == 'uniform_resource_identifier': return name.chosen[0].chosen.native return None
[ "def", "_get_crl_url", "(", "self", ",", "distribution_points", ")", ":", "if", "distribution_points", "is", "None", ":", "return", "None", "for", "distribution_point", "in", "distribution_points", ":", "name", "=", "distribution_point", "[", "'distribution_point'", "]", "if", "name", ".", "name", "==", "'full_name'", "and", "name", ".", "chosen", "[", "0", "]", ".", "name", "==", "'uniform_resource_identifier'", ":", "return", "name", ".", "chosen", "[", "0", "]", ".", "chosen", ".", "native", "return", "None" ]
Grabs the first URL out of a asn1crypto.x509.CRLDistributionPoints object :param distribution_points: The x509.CRLDistributionPoints object to pull the URL out of :return: A unicode string or None
[ "Grabs", "the", "first", "URL", "out", "of", "a", "asn1crypto", ".", "x509", ".", "CRLDistributionPoints", "object" ]
969dae884fa7f73988bbf1dcbec4fb51e234a3c5
https://github.com/wbond/certbuilder/blob/969dae884fa7f73988bbf1dcbec4fb51e234a3c5/certbuilder/__init__.py#L544-L564
train
wbond/certbuilder
certbuilder/__init__.py
CertificateBuilder.ocsp_no_check
def ocsp_no_check(self, value): """ A bool - if the certificate should have the OCSP no check extension. Only applicable to certificates created for signing OCSP responses. Such certificates should normally be issued for a very short period of time since they are effectively whitelisted by clients. """ if value is None: self._ocsp_no_check = None else: self._ocsp_no_check = bool(value)
python
def ocsp_no_check(self, value): """ A bool - if the certificate should have the OCSP no check extension. Only applicable to certificates created for signing OCSP responses. Such certificates should normally be issued for a very short period of time since they are effectively whitelisted by clients. """ if value is None: self._ocsp_no_check = None else: self._ocsp_no_check = bool(value)
[ "def", "ocsp_no_check", "(", "self", ",", "value", ")", ":", "if", "value", "is", "None", ":", "self", ".", "_ocsp_no_check", "=", "None", "else", ":", "self", ".", "_ocsp_no_check", "=", "bool", "(", "value", ")" ]
A bool - if the certificate should have the OCSP no check extension. Only applicable to certificates created for signing OCSP responses. Such certificates should normally be issued for a very short period of time since they are effectively whitelisted by clients.
[ "A", "bool", "-", "if", "the", "certificate", "should", "have", "the", "OCSP", "no", "check", "extension", ".", "Only", "applicable", "to", "certificates", "created", "for", "signing", "OCSP", "responses", ".", "Such", "certificates", "should", "normally", "be", "issued", "for", "a", "very", "short", "period", "of", "time", "since", "they", "are", "effectively", "whitelisted", "by", "clients", "." ]
969dae884fa7f73988bbf1dcbec4fb51e234a3c5
https://github.com/wbond/certbuilder/blob/969dae884fa7f73988bbf1dcbec4fb51e234a3c5/certbuilder/__init__.py#L688-L699
train
tell-k/django-modelsdoc
modelsdoc/templatetags/modelsdoc_tags.py
emptylineless
def emptylineless(parser, token): """ Removes empty line. Example usage:: {% emptylineless %} test1 test2 test3 {% endemptylineless %} This example would return this HTML:: test1 test2 test3 """ nodelist = parser.parse(('endemptylineless',)) parser.delete_first_token() return EmptylinelessNode(nodelist)
python
def emptylineless(parser, token): """ Removes empty line. Example usage:: {% emptylineless %} test1 test2 test3 {% endemptylineless %} This example would return this HTML:: test1 test2 test3 """ nodelist = parser.parse(('endemptylineless',)) parser.delete_first_token() return EmptylinelessNode(nodelist)
[ "def", "emptylineless", "(", "parser", ",", "token", ")", ":", "nodelist", "=", "parser", ".", "parse", "(", "(", "'endemptylineless'", ",", ")", ")", "parser", ".", "delete_first_token", "(", ")", "return", "EmptylinelessNode", "(", "nodelist", ")" ]
Removes empty line. Example usage:: {% emptylineless %} test1 test2 test3 {% endemptylineless %} This example would return this HTML:: test1 test2 test3
[ "Removes", "empty", "line", "." ]
c9d336e76251feb142347b3a41365430d3365436
https://github.com/tell-k/django-modelsdoc/blob/c9d336e76251feb142347b3a41365430d3365436/modelsdoc/templatetags/modelsdoc_tags.py#L31-L54
train
justquick/python-varnish
varnish.py
http_purge_url
def http_purge_url(url): """ Do an HTTP PURGE of the given asset. The URL is run through urlparse and must point to the varnish instance not the varnishadm """ url = urlparse(url) connection = HTTPConnection(url.hostname, url.port or 80) path = url.path or '/' connection.request('PURGE', '%s?%s' % (path, url.query) if url.query else path, '', {'Host': '%s:%s' % (url.hostname, url.port) if url.port else url.hostname}) response = connection.getresponse() if response.status != 200: logging.error('Purge failed with status: %s' % response.status) return response
python
def http_purge_url(url): """ Do an HTTP PURGE of the given asset. The URL is run through urlparse and must point to the varnish instance not the varnishadm """ url = urlparse(url) connection = HTTPConnection(url.hostname, url.port or 80) path = url.path or '/' connection.request('PURGE', '%s?%s' % (path, url.query) if url.query else path, '', {'Host': '%s:%s' % (url.hostname, url.port) if url.port else url.hostname}) response = connection.getresponse() if response.status != 200: logging.error('Purge failed with status: %s' % response.status) return response
[ "def", "http_purge_url", "(", "url", ")", ":", "url", "=", "urlparse", "(", "url", ")", "connection", "=", "HTTPConnection", "(", "url", ".", "hostname", ",", "url", ".", "port", "or", "80", ")", "path", "=", "url", ".", "path", "or", "'/'", "connection", ".", "request", "(", "'PURGE'", ",", "'%s?%s'", "%", "(", "path", ",", "url", ".", "query", ")", "if", "url", ".", "query", "else", "path", ",", "''", ",", "{", "'Host'", ":", "'%s:%s'", "%", "(", "url", ".", "hostname", ",", "url", ".", "port", ")", "if", "url", ".", "port", "else", "url", ".", "hostname", "}", ")", "response", "=", "connection", ".", "getresponse", "(", ")", "if", "response", ".", "status", "!=", "200", ":", "logging", ".", "error", "(", "'Purge failed with status: %s'", "%", "response", ".", "status", ")", "return", "response" ]
Do an HTTP PURGE of the given asset. The URL is run through urlparse and must point to the varnish instance not the varnishadm
[ "Do", "an", "HTTP", "PURGE", "of", "the", "given", "asset", ".", "The", "URL", "is", "run", "through", "urlparse", "and", "must", "point", "to", "the", "varnish", "instance", "not", "the", "varnishadm" ]
8f114c74898e6c5ade2ce49c8b595040bd150465
https://github.com/justquick/python-varnish/blob/8f114c74898e6c5ade2ce49c8b595040bd150465/varnish.py#L47-L60
train
justquick/python-varnish
varnish.py
run
def run(addr, *commands, **kwargs): """ Non-threaded batch command runner returning output results """ results = [] handler = VarnishHandler(addr, **kwargs) for cmd in commands: if isinstance(cmd, tuple) and len(cmd)>1: results.extend([getattr(handler, c[0].replace('.','_'))(*c[1:]) for c in cmd]) else: results.append(getattr(handler, cmd.replace('.','_'))(*commands[1:])) break handler.close() return results
python
def run(addr, *commands, **kwargs): """ Non-threaded batch command runner returning output results """ results = [] handler = VarnishHandler(addr, **kwargs) for cmd in commands: if isinstance(cmd, tuple) and len(cmd)>1: results.extend([getattr(handler, c[0].replace('.','_'))(*c[1:]) for c in cmd]) else: results.append(getattr(handler, cmd.replace('.','_'))(*commands[1:])) break handler.close() return results
[ "def", "run", "(", "addr", ",", "*", "commands", ",", "*", "*", "kwargs", ")", ":", "results", "=", "[", "]", "handler", "=", "VarnishHandler", "(", "addr", ",", "*", "*", "kwargs", ")", "for", "cmd", "in", "commands", ":", "if", "isinstance", "(", "cmd", ",", "tuple", ")", "and", "len", "(", "cmd", ")", ">", "1", ":", "results", ".", "extend", "(", "[", "getattr", "(", "handler", ",", "c", "[", "0", "]", ".", "replace", "(", "'.'", ",", "'_'", ")", ")", "(", "*", "c", "[", "1", ":", "]", ")", "for", "c", "in", "cmd", "]", ")", "else", ":", "results", ".", "append", "(", "getattr", "(", "handler", ",", "cmd", ".", "replace", "(", "'.'", ",", "'_'", ")", ")", "(", "*", "commands", "[", "1", ":", "]", ")", ")", "break", "handler", ".", "close", "(", ")", "return", "results" ]
Non-threaded batch command runner returning output results
[ "Non", "-", "threaded", "batch", "command", "runner", "returning", "output", "results" ]
8f114c74898e6c5ade2ce49c8b595040bd150465
https://github.com/justquick/python-varnish/blob/8f114c74898e6c5ade2ce49c8b595040bd150465/varnish.py#L289-L302
train
madeindjs/Super-Markdown
SuperMarkdown/SuperMarkdown.py
SuperMarkdown.add_stylesheets
def add_stylesheets(self, *css_files): """add stylesheet files in HTML head""" for css_file in css_files: self.main_soup.style.append(self._text_file(css_file))
python
def add_stylesheets(self, *css_files): """add stylesheet files in HTML head""" for css_file in css_files: self.main_soup.style.append(self._text_file(css_file))
[ "def", "add_stylesheets", "(", "self", ",", "*", "css_files", ")", ":", "for", "css_file", "in", "css_files", ":", "self", ".", "main_soup", ".", "style", ".", "append", "(", "self", ".", "_text_file", "(", "css_file", ")", ")" ]
add stylesheet files in HTML head
[ "add", "stylesheet", "files", "in", "HTML", "head" ]
fe2da746afa6a27aaaad27a2db1dca234f802eb0
https://github.com/madeindjs/Super-Markdown/blob/fe2da746afa6a27aaaad27a2db1dca234f802eb0/SuperMarkdown/SuperMarkdown.py#L43-L46
train
madeindjs/Super-Markdown
SuperMarkdown/SuperMarkdown.py
SuperMarkdown.add_javascripts
def add_javascripts(self, *js_files): """add javascripts files in HTML body""" # create the script tag if don't exists if self.main_soup.script is None: script_tag = self.main_soup.new_tag('script') self.main_soup.body.append(script_tag) for js_file in js_files: self.main_soup.script.append(self._text_file(js_file))
python
def add_javascripts(self, *js_files): """add javascripts files in HTML body""" # create the script tag if don't exists if self.main_soup.script is None: script_tag = self.main_soup.new_tag('script') self.main_soup.body.append(script_tag) for js_file in js_files: self.main_soup.script.append(self._text_file(js_file))
[ "def", "add_javascripts", "(", "self", ",", "*", "js_files", ")", ":", "# create the script tag if don't exists", "if", "self", ".", "main_soup", ".", "script", "is", "None", ":", "script_tag", "=", "self", ".", "main_soup", ".", "new_tag", "(", "'script'", ")", "self", ".", "main_soup", ".", "body", ".", "append", "(", "script_tag", ")", "for", "js_file", "in", "js_files", ":", "self", ".", "main_soup", ".", "script", ".", "append", "(", "self", ".", "_text_file", "(", "js_file", ")", ")" ]
add javascripts files in HTML body
[ "add", "javascripts", "files", "in", "HTML", "body" ]
fe2da746afa6a27aaaad27a2db1dca234f802eb0
https://github.com/madeindjs/Super-Markdown/blob/fe2da746afa6a27aaaad27a2db1dca234f802eb0/SuperMarkdown/SuperMarkdown.py#L48-L56
train
madeindjs/Super-Markdown
SuperMarkdown/SuperMarkdown.py
SuperMarkdown.export
def export(self): """return the object in a file""" with open(self.export_url, 'w', encoding='utf-8') as file: file.write(self.build()) if self.open_browser: webbrowser.open_new_tab(self.export_url)
python
def export(self): """return the object in a file""" with open(self.export_url, 'w', encoding='utf-8') as file: file.write(self.build()) if self.open_browser: webbrowser.open_new_tab(self.export_url)
[ "def", "export", "(", "self", ")", ":", "with", "open", "(", "self", ".", "export_url", ",", "'w'", ",", "encoding", "=", "'utf-8'", ")", "as", "file", ":", "file", ".", "write", "(", "self", ".", "build", "(", ")", ")", "if", "self", ".", "open_browser", ":", "webbrowser", ".", "open_new_tab", "(", "self", ".", "export_url", ")" ]
return the object in a file
[ "return", "the", "object", "in", "a", "file" ]
fe2da746afa6a27aaaad27a2db1dca234f802eb0
https://github.com/madeindjs/Super-Markdown/blob/fe2da746afa6a27aaaad27a2db1dca234f802eb0/SuperMarkdown/SuperMarkdown.py#L58-L64
train
madeindjs/Super-Markdown
SuperMarkdown/SuperMarkdown.py
SuperMarkdown.build
def build(self): """convert Markdown text as html. return the html file as string""" markdown_html = markdown.markdown(self.markdown_text, extensions=[ TocExtension(), 'fenced_code', 'markdown_checklist.extension', 'markdown.extensions.tables']) markdown_soup = BeautifulSoup(markdown_html, 'html.parser') # include jquery & mermaid.js only if there are Mermaid graph if markdown_soup.find('code', attrs={'class': 'mermaid'}): self._add_mermaid_js() # search in markdown html if there are Dot Graph & replace it with .svg result for dot_tag in markdown_soup.find_all('code', attrs={'class': 'dotgraph'}): grap_svg = self._text_to_graphiz(dot_tag.string) graph_soup = BeautifulSoup(grap_svg, 'html.parser') dot_tag.parent.replaceWith(graph_soup) self.main_soup.body.append(markdown_soup) return self.main_soup.prettify()
python
def build(self): """convert Markdown text as html. return the html file as string""" markdown_html = markdown.markdown(self.markdown_text, extensions=[ TocExtension(), 'fenced_code', 'markdown_checklist.extension', 'markdown.extensions.tables']) markdown_soup = BeautifulSoup(markdown_html, 'html.parser') # include jquery & mermaid.js only if there are Mermaid graph if markdown_soup.find('code', attrs={'class': 'mermaid'}): self._add_mermaid_js() # search in markdown html if there are Dot Graph & replace it with .svg result for dot_tag in markdown_soup.find_all('code', attrs={'class': 'dotgraph'}): grap_svg = self._text_to_graphiz(dot_tag.string) graph_soup = BeautifulSoup(grap_svg, 'html.parser') dot_tag.parent.replaceWith(graph_soup) self.main_soup.body.append(markdown_soup) return self.main_soup.prettify()
[ "def", "build", "(", "self", ")", ":", "markdown_html", "=", "markdown", ".", "markdown", "(", "self", ".", "markdown_text", ",", "extensions", "=", "[", "TocExtension", "(", ")", ",", "'fenced_code'", ",", "'markdown_checklist.extension'", ",", "'markdown.extensions.tables'", "]", ")", "markdown_soup", "=", "BeautifulSoup", "(", "markdown_html", ",", "'html.parser'", ")", "# include jquery & mermaid.js only if there are Mermaid graph", "if", "markdown_soup", ".", "find", "(", "'code'", ",", "attrs", "=", "{", "'class'", ":", "'mermaid'", "}", ")", ":", "self", ".", "_add_mermaid_js", "(", ")", "# search in markdown html if there are Dot Graph & replace it with .svg result", "for", "dot_tag", "in", "markdown_soup", ".", "find_all", "(", "'code'", ",", "attrs", "=", "{", "'class'", ":", "'dotgraph'", "}", ")", ":", "grap_svg", "=", "self", ".", "_text_to_graphiz", "(", "dot_tag", ".", "string", ")", "graph_soup", "=", "BeautifulSoup", "(", "grap_svg", ",", "'html.parser'", ")", "dot_tag", ".", "parent", ".", "replaceWith", "(", "graph_soup", ")", "self", ".", "main_soup", ".", "body", ".", "append", "(", "markdown_soup", ")", "return", "self", ".", "main_soup", ".", "prettify", "(", ")" ]
convert Markdown text as html. return the html file as string
[ "convert", "Markdown", "text", "as", "html", ".", "return", "the", "html", "file", "as", "string" ]
fe2da746afa6a27aaaad27a2db1dca234f802eb0
https://github.com/madeindjs/Super-Markdown/blob/fe2da746afa6a27aaaad27a2db1dca234f802eb0/SuperMarkdown/SuperMarkdown.py#L66-L84
train
madeindjs/Super-Markdown
SuperMarkdown/SuperMarkdown.py
SuperMarkdown._text_file
def _text_file(self, url): """return the content of a file""" try: with open(url, 'r', encoding='utf-8') as file: return file.read() except FileNotFoundError: print('File `{}` not found'.format(url)) sys.exit(0)
python
def _text_file(self, url): """return the content of a file""" try: with open(url, 'r', encoding='utf-8') as file: return file.read() except FileNotFoundError: print('File `{}` not found'.format(url)) sys.exit(0)
[ "def", "_text_file", "(", "self", ",", "url", ")", ":", "try", ":", "with", "open", "(", "url", ",", "'r'", ",", "encoding", "=", "'utf-8'", ")", "as", "file", ":", "return", "file", ".", "read", "(", ")", "except", "FileNotFoundError", ":", "print", "(", "'File `{}` not found'", ".", "format", "(", "url", ")", ")", "sys", ".", "exit", "(", "0", ")" ]
return the content of a file
[ "return", "the", "content", "of", "a", "file" ]
fe2da746afa6a27aaaad27a2db1dca234f802eb0
https://github.com/madeindjs/Super-Markdown/blob/fe2da746afa6a27aaaad27a2db1dca234f802eb0/SuperMarkdown/SuperMarkdown.py#L86-L93
train
madeindjs/Super-Markdown
SuperMarkdown/SuperMarkdown.py
SuperMarkdown._text_to_graphiz
def _text_to_graphiz(self, text): """create a graphviz graph from text""" dot = Source(text, format='svg') return dot.pipe().decode('utf-8')
python
def _text_to_graphiz(self, text): """create a graphviz graph from text""" dot = Source(text, format='svg') return dot.pipe().decode('utf-8')
[ "def", "_text_to_graphiz", "(", "self", ",", "text", ")", ":", "dot", "=", "Source", "(", "text", ",", "format", "=", "'svg'", ")", "return", "dot", ".", "pipe", "(", ")", ".", "decode", "(", "'utf-8'", ")" ]
create a graphviz graph from text
[ "create", "a", "graphviz", "graph", "from", "text" ]
fe2da746afa6a27aaaad27a2db1dca234f802eb0
https://github.com/madeindjs/Super-Markdown/blob/fe2da746afa6a27aaaad27a2db1dca234f802eb0/SuperMarkdown/SuperMarkdown.py#L95-L98
train
madeindjs/Super-Markdown
SuperMarkdown/SuperMarkdown.py
SuperMarkdown._add_mermaid_js
def _add_mermaid_js(self): """add js libraries and css files of mermaid js_file""" self.add_javascripts('{}/js/jquery-1.11.3.min.js'.format(self.resources_path)) self.add_javascripts('{}/js/mermaid.min.js'.format(self.resources_path)) self.add_stylesheets('{}/css/mermaid.css'.format(self.resources_path)) self.main_soup.script.append('mermaid.initialize({startOnLoad:true });')
python
def _add_mermaid_js(self): """add js libraries and css files of mermaid js_file""" self.add_javascripts('{}/js/jquery-1.11.3.min.js'.format(self.resources_path)) self.add_javascripts('{}/js/mermaid.min.js'.format(self.resources_path)) self.add_stylesheets('{}/css/mermaid.css'.format(self.resources_path)) self.main_soup.script.append('mermaid.initialize({startOnLoad:true });')
[ "def", "_add_mermaid_js", "(", "self", ")", ":", "self", ".", "add_javascripts", "(", "'{}/js/jquery-1.11.3.min.js'", ".", "format", "(", "self", ".", "resources_path", ")", ")", "self", ".", "add_javascripts", "(", "'{}/js/mermaid.min.js'", ".", "format", "(", "self", ".", "resources_path", ")", ")", "self", ".", "add_stylesheets", "(", "'{}/css/mermaid.css'", ".", "format", "(", "self", ".", "resources_path", ")", ")", "self", ".", "main_soup", ".", "script", ".", "append", "(", "'mermaid.initialize({startOnLoad:true });'", ")" ]
add js libraries and css files of mermaid js_file
[ "add", "js", "libraries", "and", "css", "files", "of", "mermaid", "js_file" ]
fe2da746afa6a27aaaad27a2db1dca234f802eb0
https://github.com/madeindjs/Super-Markdown/blob/fe2da746afa6a27aaaad27a2db1dca234f802eb0/SuperMarkdown/SuperMarkdown.py#L100-L105
train
paul-wolf/strgen
strgen/__init__.py
StringGenerator.getCharacterSet
def getCharacterSet(self): '''Get a character set with individual members or ranges. Current index is on '[', the start of the character set. ''' chars = u'' c = None cnt = 1 start = 0 while True: escaped_slash = False c = self.next() # print "pattern : ", self.pattern # print "C : ", c # print "Slash : ", c == u'\\' # print 'chars : ', chars # print 'index : ', self.index # print 'last : ', self.last() # print 'lookahead : ', self.lookahead() if self.lookahead() == u'-' and not c == u'\\': f = c self.next() # skip hyphen c = self.next() # get far range if not c or (c in self.meta_chars): raise StringGenerator.SyntaxError(u"unexpected end of class range") chars += self.getCharacterRange(f, c) elif c == u'\\': if self.lookahead() in self.meta_chars: c = self.next() chars += c continue elif self.lookahead() in self.string_code: c = self.next() chars += self.string_code[c] elif c and c not in self.meta_chars: chars += c if c == u']': if self.lookahead() == u'{': [start, cnt] = self.getQuantifier() else: start = -1 cnt = 1 break if c and c in self.meta_chars and not self.last() == u"\\": raise StringGenerator.SyntaxError(u"Un-escaped character in class definition: %s" % c) if not c: break return StringGenerator.CharacterSet(chars, start, cnt)
python
def getCharacterSet(self): '''Get a character set with individual members or ranges. Current index is on '[', the start of the character set. ''' chars = u'' c = None cnt = 1 start = 0 while True: escaped_slash = False c = self.next() # print "pattern : ", self.pattern # print "C : ", c # print "Slash : ", c == u'\\' # print 'chars : ', chars # print 'index : ', self.index # print 'last : ', self.last() # print 'lookahead : ', self.lookahead() if self.lookahead() == u'-' and not c == u'\\': f = c self.next() # skip hyphen c = self.next() # get far range if not c or (c in self.meta_chars): raise StringGenerator.SyntaxError(u"unexpected end of class range") chars += self.getCharacterRange(f, c) elif c == u'\\': if self.lookahead() in self.meta_chars: c = self.next() chars += c continue elif self.lookahead() in self.string_code: c = self.next() chars += self.string_code[c] elif c and c not in self.meta_chars: chars += c if c == u']': if self.lookahead() == u'{': [start, cnt] = self.getQuantifier() else: start = -1 cnt = 1 break if c and c in self.meta_chars and not self.last() == u"\\": raise StringGenerator.SyntaxError(u"Un-escaped character in class definition: %s" % c) if not c: break return StringGenerator.CharacterSet(chars, start, cnt)
[ "def", "getCharacterSet", "(", "self", ")", ":", "chars", "=", "u''", "c", "=", "None", "cnt", "=", "1", "start", "=", "0", "while", "True", ":", "escaped_slash", "=", "False", "c", "=", "self", ".", "next", "(", ")", "# print \"pattern : \", self.pattern", "# print \"C : \", c", "# print \"Slash : \", c == u'\\\\'", "# print 'chars : ', chars", "# print 'index : ', self.index", "# print 'last : ', self.last()", "# print 'lookahead : ', self.lookahead()", "if", "self", ".", "lookahead", "(", ")", "==", "u'-'", "and", "not", "c", "==", "u'\\\\'", ":", "f", "=", "c", "self", ".", "next", "(", ")", "# skip hyphen", "c", "=", "self", ".", "next", "(", ")", "# get far range", "if", "not", "c", "or", "(", "c", "in", "self", ".", "meta_chars", ")", ":", "raise", "StringGenerator", ".", "SyntaxError", "(", "u\"unexpected end of class range\"", ")", "chars", "+=", "self", ".", "getCharacterRange", "(", "f", ",", "c", ")", "elif", "c", "==", "u'\\\\'", ":", "if", "self", ".", "lookahead", "(", ")", "in", "self", ".", "meta_chars", ":", "c", "=", "self", ".", "next", "(", ")", "chars", "+=", "c", "continue", "elif", "self", ".", "lookahead", "(", ")", "in", "self", ".", "string_code", ":", "c", "=", "self", ".", "next", "(", ")", "chars", "+=", "self", ".", "string_code", "[", "c", "]", "elif", "c", "and", "c", "not", "in", "self", ".", "meta_chars", ":", "chars", "+=", "c", "if", "c", "==", "u']'", ":", "if", "self", ".", "lookahead", "(", ")", "==", "u'{'", ":", "[", "start", ",", "cnt", "]", "=", "self", ".", "getQuantifier", "(", ")", "else", ":", "start", "=", "-", "1", "cnt", "=", "1", "break", "if", "c", "and", "c", "in", "self", ".", "meta_chars", "and", "not", "self", ".", "last", "(", ")", "==", "u\"\\\\\"", ":", "raise", "StringGenerator", ".", "SyntaxError", "(", "u\"Un-escaped character in class definition: %s\"", "%", "c", ")", "if", "not", "c", ":", "break", "return", "StringGenerator", ".", "CharacterSet", "(", "chars", ",", "start", ",", "cnt", ")" ]
Get a character set with individual members or ranges. Current index is on '[', the start of the character set.
[ "Get", "a", "character", "set", "with", "individual", "members", "or", "ranges", "." ]
ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f
https://github.com/paul-wolf/strgen/blob/ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f/strgen/__init__.py#L368-L419
train
paul-wolf/strgen
strgen/__init__.py
StringGenerator.getLiteral
def getLiteral(self): '''Get a sequence of non-special characters.''' # we are on the first non-special character chars = u'' c = self.current() while True: if c and c == u"\\": c = self.next() if c: chars += c continue elif not c or (c in self.meta_chars): break else: chars += c if self.lookahead() and self.lookahead() in self.meta_chars: break c = self.next() return StringGenerator.Literal(chars)
python
def getLiteral(self): '''Get a sequence of non-special characters.''' # we are on the first non-special character chars = u'' c = self.current() while True: if c and c == u"\\": c = self.next() if c: chars += c continue elif not c or (c in self.meta_chars): break else: chars += c if self.lookahead() and self.lookahead() in self.meta_chars: break c = self.next() return StringGenerator.Literal(chars)
[ "def", "getLiteral", "(", "self", ")", ":", "# we are on the first non-special character", "chars", "=", "u''", "c", "=", "self", ".", "current", "(", ")", "while", "True", ":", "if", "c", "and", "c", "==", "u\"\\\\\"", ":", "c", "=", "self", ".", "next", "(", ")", "if", "c", ":", "chars", "+=", "c", "continue", "elif", "not", "c", "or", "(", "c", "in", "self", ".", "meta_chars", ")", ":", "break", "else", ":", "chars", "+=", "c", "if", "self", ".", "lookahead", "(", ")", "and", "self", ".", "lookahead", "(", ")", "in", "self", ".", "meta_chars", ":", "break", "c", "=", "self", ".", "next", "(", ")", "return", "StringGenerator", ".", "Literal", "(", "chars", ")" ]
Get a sequence of non-special characters.
[ "Get", "a", "sequence", "of", "non", "-", "special", "characters", "." ]
ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f
https://github.com/paul-wolf/strgen/blob/ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f/strgen/__init__.py#L421-L439
train
paul-wolf/strgen
strgen/__init__.py
StringGenerator.getSequence
def getSequence(self, level=0): '''Get a sequence of nodes.''' seq = [] op = '' left_operand = None right_operand = None sequence_closed = False while True: c = self.next() if not c: break if c and c not in self.meta_chars: seq.append(self.getLiteral()) elif c and c == u'$' and self.lookahead() == u'{': seq.append(self.getSource()) elif c == u'[' and not self.last() == u'\\': seq.append(self.getCharacterSet()) elif c == u'(' and not self.last() == u'\\': seq.append(self.getSequence(level + 1)) elif c == u')' and not self.last() == u'\\': # end of this sequence if level == 0: # there should be no parens here raise StringGenerator.SyntaxError(u"Extra closing parenthesis") sequence_closed = True break elif c == u'|' and not self.last() == u'\\': op = c elif c == u'&' and not self.last() == u'\\': op = c else: if c in self.meta_chars and not self.last() == u"\\": raise StringGenerator.SyntaxError(u"Un-escaped special character: %s" % c) #print( op,len(seq) ) if op and not left_operand: if not seq or len(seq) < 1: raise StringGenerator.SyntaxError(u"Operator: %s with no left operand" % op) left_operand = seq.pop() elif op and len(seq) >= 1 and left_operand: right_operand = seq.pop() #print( "popped: [%s] %s:%s"%( op, left_operand, right_operand) ) if op == u'|': seq.append(StringGenerator.SequenceOR([left_operand, right_operand])) elif op == u'&': seq.append(StringGenerator.SequenceAND([left_operand, right_operand])) op = u'' left_operand = None right_operand = None # check for syntax errors if op: raise StringGenerator.SyntaxError(u"Operator: %s with no right operand" % op) if level > 0 and not sequence_closed: # it means we are finishing a non-first-level sequence without closing parens raise StringGenerator.SyntaxError(u"Missing closing parenthesis") return StringGenerator.Sequence(seq)
python
def getSequence(self, level=0): '''Get a sequence of nodes.''' seq = [] op = '' left_operand = None right_operand = None sequence_closed = False while True: c = self.next() if not c: break if c and c not in self.meta_chars: seq.append(self.getLiteral()) elif c and c == u'$' and self.lookahead() == u'{': seq.append(self.getSource()) elif c == u'[' and not self.last() == u'\\': seq.append(self.getCharacterSet()) elif c == u'(' and not self.last() == u'\\': seq.append(self.getSequence(level + 1)) elif c == u')' and not self.last() == u'\\': # end of this sequence if level == 0: # there should be no parens here raise StringGenerator.SyntaxError(u"Extra closing parenthesis") sequence_closed = True break elif c == u'|' and not self.last() == u'\\': op = c elif c == u'&' and not self.last() == u'\\': op = c else: if c in self.meta_chars and not self.last() == u"\\": raise StringGenerator.SyntaxError(u"Un-escaped special character: %s" % c) #print( op,len(seq) ) if op and not left_operand: if not seq or len(seq) < 1: raise StringGenerator.SyntaxError(u"Operator: %s with no left operand" % op) left_operand = seq.pop() elif op and len(seq) >= 1 and left_operand: right_operand = seq.pop() #print( "popped: [%s] %s:%s"%( op, left_operand, right_operand) ) if op == u'|': seq.append(StringGenerator.SequenceOR([left_operand, right_operand])) elif op == u'&': seq.append(StringGenerator.SequenceAND([left_operand, right_operand])) op = u'' left_operand = None right_operand = None # check for syntax errors if op: raise StringGenerator.SyntaxError(u"Operator: %s with no right operand" % op) if level > 0 and not sequence_closed: # it means we are finishing a non-first-level sequence without closing parens raise StringGenerator.SyntaxError(u"Missing closing parenthesis") return StringGenerator.Sequence(seq)
[ "def", "getSequence", "(", "self", ",", "level", "=", "0", ")", ":", "seq", "=", "[", "]", "op", "=", "''", "left_operand", "=", "None", "right_operand", "=", "None", "sequence_closed", "=", "False", "while", "True", ":", "c", "=", "self", ".", "next", "(", ")", "if", "not", "c", ":", "break", "if", "c", "and", "c", "not", "in", "self", ".", "meta_chars", ":", "seq", ".", "append", "(", "self", ".", "getLiteral", "(", ")", ")", "elif", "c", "and", "c", "==", "u'$'", "and", "self", ".", "lookahead", "(", ")", "==", "u'{'", ":", "seq", ".", "append", "(", "self", ".", "getSource", "(", ")", ")", "elif", "c", "==", "u'['", "and", "not", "self", ".", "last", "(", ")", "==", "u'\\\\'", ":", "seq", ".", "append", "(", "self", ".", "getCharacterSet", "(", ")", ")", "elif", "c", "==", "u'('", "and", "not", "self", ".", "last", "(", ")", "==", "u'\\\\'", ":", "seq", ".", "append", "(", "self", ".", "getSequence", "(", "level", "+", "1", ")", ")", "elif", "c", "==", "u')'", "and", "not", "self", ".", "last", "(", ")", "==", "u'\\\\'", ":", "# end of this sequence", "if", "level", "==", "0", ":", "# there should be no parens here", "raise", "StringGenerator", ".", "SyntaxError", "(", "u\"Extra closing parenthesis\"", ")", "sequence_closed", "=", "True", "break", "elif", "c", "==", "u'|'", "and", "not", "self", ".", "last", "(", ")", "==", "u'\\\\'", ":", "op", "=", "c", "elif", "c", "==", "u'&'", "and", "not", "self", ".", "last", "(", ")", "==", "u'\\\\'", ":", "op", "=", "c", "else", ":", "if", "c", "in", "self", ".", "meta_chars", "and", "not", "self", ".", "last", "(", ")", "==", "u\"\\\\\"", ":", "raise", "StringGenerator", ".", "SyntaxError", "(", "u\"Un-escaped special character: %s\"", "%", "c", ")", "#print( op,len(seq) )", "if", "op", "and", "not", "left_operand", ":", "if", "not", "seq", "or", "len", "(", "seq", ")", "<", "1", ":", "raise", "StringGenerator", ".", "SyntaxError", "(", "u\"Operator: %s with no left operand\"", "%", "op", ")", "left_operand", "=", "seq", ".", "pop", "(", ")", "elif", "op", "and", "len", "(", "seq", ")", ">=", "1", "and", "left_operand", ":", "right_operand", "=", "seq", ".", "pop", "(", ")", "#print( \"popped: [%s] %s:%s\"%( op, left_operand, right_operand) )", "if", "op", "==", "u'|'", ":", "seq", ".", "append", "(", "StringGenerator", ".", "SequenceOR", "(", "[", "left_operand", ",", "right_operand", "]", ")", ")", "elif", "op", "==", "u'&'", ":", "seq", ".", "append", "(", "StringGenerator", ".", "SequenceAND", "(", "[", "left_operand", ",", "right_operand", "]", ")", ")", "op", "=", "u''", "left_operand", "=", "None", "right_operand", "=", "None", "# check for syntax errors", "if", "op", ":", "raise", "StringGenerator", ".", "SyntaxError", "(", "u\"Operator: %s with no right operand\"", "%", "op", ")", "if", "level", ">", "0", "and", "not", "sequence_closed", ":", "# it means we are finishing a non-first-level sequence without closing parens", "raise", "StringGenerator", ".", "SyntaxError", "(", "u\"Missing closing parenthesis\"", ")", "return", "StringGenerator", ".", "Sequence", "(", "seq", ")" ]
Get a sequence of nodes.
[ "Get", "a", "sequence", "of", "nodes", "." ]
ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f
https://github.com/paul-wolf/strgen/blob/ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f/strgen/__init__.py#L441-L501
train
paul-wolf/strgen
strgen/__init__.py
StringGenerator.dump
def dump(self, **kwargs): import sys '''Print the parse tree and then call render for an example.''' if not self.seq: self.seq = self.getSequence() print("StringGenerator version: %s" % (__version__)) print("Python version: %s" % sys.version) # this doesn't work anymore in p3 # print("Random method provider class: %s" % randint.im_class.__name__) self.seq.dump() return self.render(**kwargs)
python
def dump(self, **kwargs): import sys '''Print the parse tree and then call render for an example.''' if not self.seq: self.seq = self.getSequence() print("StringGenerator version: %s" % (__version__)) print("Python version: %s" % sys.version) # this doesn't work anymore in p3 # print("Random method provider class: %s" % randint.im_class.__name__) self.seq.dump() return self.render(**kwargs)
[ "def", "dump", "(", "self", ",", "*", "*", "kwargs", ")", ":", "import", "sys", "if", "not", "self", ".", "seq", ":", "self", ".", "seq", "=", "self", ".", "getSequence", "(", ")", "print", "(", "\"StringGenerator version: %s\"", "%", "(", "__version__", ")", ")", "print", "(", "\"Python version: %s\"", "%", "sys", ".", "version", ")", "# this doesn't work anymore in p3", "# print(\"Random method provider class: %s\" % randint.im_class.__name__)", "self", ".", "seq", ".", "dump", "(", ")", "return", "self", ".", "render", "(", "*", "*", "kwargs", ")" ]
Print the parse tree and then call render for an example.
[ "Print", "the", "parse", "tree", "and", "then", "call", "render", "for", "an", "example", "." ]
ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f
https://github.com/paul-wolf/strgen/blob/ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f/strgen/__init__.py#L521-L531
train
paul-wolf/strgen
strgen/__init__.py
StringGenerator.render_list
def render_list(self, cnt, unique=False, progress_callback=None, **kwargs): '''Return a list of generated strings. Args: cnt (int): length of list unique (bool): whether to make entries unique Returns: list. We keep track of total attempts because a template may specify something impossible to attain, like [1-9]{} with cnt==1000 ''' rendered_list = [] i = 0 total_attempts = 0 while True: if i >= cnt: break if total_attempts > cnt * self.unique_attempts_factor: raise StringGenerator.UniquenessError(u"couldn't satisfy uniqueness") s = self.render(**kwargs) if unique: if not s in rendered_list: rendered_list.append(s) i += 1 else: rendered_list.append(s) i += 1 total_attempts += 1 # Optionally trigger the progress indicator to inform others about our progress if progress_callback and callable(progress_callback): progress_callback(i, cnt) return rendered_list
python
def render_list(self, cnt, unique=False, progress_callback=None, **kwargs): '''Return a list of generated strings. Args: cnt (int): length of list unique (bool): whether to make entries unique Returns: list. We keep track of total attempts because a template may specify something impossible to attain, like [1-9]{} with cnt==1000 ''' rendered_list = [] i = 0 total_attempts = 0 while True: if i >= cnt: break if total_attempts > cnt * self.unique_attempts_factor: raise StringGenerator.UniquenessError(u"couldn't satisfy uniqueness") s = self.render(**kwargs) if unique: if not s in rendered_list: rendered_list.append(s) i += 1 else: rendered_list.append(s) i += 1 total_attempts += 1 # Optionally trigger the progress indicator to inform others about our progress if progress_callback and callable(progress_callback): progress_callback(i, cnt) return rendered_list
[ "def", "render_list", "(", "self", ",", "cnt", ",", "unique", "=", "False", ",", "progress_callback", "=", "None", ",", "*", "*", "kwargs", ")", ":", "rendered_list", "=", "[", "]", "i", "=", "0", "total_attempts", "=", "0", "while", "True", ":", "if", "i", ">=", "cnt", ":", "break", "if", "total_attempts", ">", "cnt", "*", "self", ".", "unique_attempts_factor", ":", "raise", "StringGenerator", ".", "UniquenessError", "(", "u\"couldn't satisfy uniqueness\"", ")", "s", "=", "self", ".", "render", "(", "*", "*", "kwargs", ")", "if", "unique", ":", "if", "not", "s", "in", "rendered_list", ":", "rendered_list", ".", "append", "(", "s", ")", "i", "+=", "1", "else", ":", "rendered_list", ".", "append", "(", "s", ")", "i", "+=", "1", "total_attempts", "+=", "1", "# Optionally trigger the progress indicator to inform others about our progress", "if", "progress_callback", "and", "callable", "(", "progress_callback", ")", ":", "progress_callback", "(", "i", ",", "cnt", ")", "return", "rendered_list" ]
Return a list of generated strings. Args: cnt (int): length of list unique (bool): whether to make entries unique Returns: list. We keep track of total attempts because a template may specify something impossible to attain, like [1-9]{} with cnt==1000
[ "Return", "a", "list", "of", "generated", "strings", "." ]
ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f
https://github.com/paul-wolf/strgen/blob/ca1a1484bed5a31dc9ceaef1ab62dd5582cc0d9f/strgen/__init__.py#L533-L570
train
seperman/s3utils
s3utils/s3utils.py
S3utils.connect
def connect(self): """ Establish the connection. This is done automatically for you. If you lose the connection, you can manually run this to be re-connected. """ self.conn = boto.connect_s3(self.AWS_ACCESS_KEY_ID, self.AWS_SECRET_ACCESS_KEY, debug=self.S3UTILS_DEBUG_LEVEL) self.bucket = self.conn.get_bucket(self.AWS_STORAGE_BUCKET_NAME) self.k = Key(self.bucket)
python
def connect(self): """ Establish the connection. This is done automatically for you. If you lose the connection, you can manually run this to be re-connected. """ self.conn = boto.connect_s3(self.AWS_ACCESS_KEY_ID, self.AWS_SECRET_ACCESS_KEY, debug=self.S3UTILS_DEBUG_LEVEL) self.bucket = self.conn.get_bucket(self.AWS_STORAGE_BUCKET_NAME) self.k = Key(self.bucket)
[ "def", "connect", "(", "self", ")", ":", "self", ".", "conn", "=", "boto", ".", "connect_s3", "(", "self", ".", "AWS_ACCESS_KEY_ID", ",", "self", ".", "AWS_SECRET_ACCESS_KEY", ",", "debug", "=", "self", ".", "S3UTILS_DEBUG_LEVEL", ")", "self", ".", "bucket", "=", "self", ".", "conn", ".", "get_bucket", "(", "self", ".", "AWS_STORAGE_BUCKET_NAME", ")", "self", ".", "k", "=", "Key", "(", "self", ".", "bucket", ")" ]
Establish the connection. This is done automatically for you. If you lose the connection, you can manually run this to be re-connected.
[ "Establish", "the", "connection", ".", "This", "is", "done", "automatically", "for", "you", "." ]
aea41388a023dcf1e95588402077e31097514cf1
https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L145-L155
train
seperman/s3utils
s3utils/s3utils.py
S3utils.connect_cloudfront
def connect_cloudfront(self): "Connect to Cloud Front. This is done automatically for you when needed." self.conn_cloudfront = connect_cloudfront(self.AWS_ACCESS_KEY_ID, self.AWS_SECRET_ACCESS_KEY, debug=self.S3UTILS_DEBUG_LEVEL)
python
def connect_cloudfront(self): "Connect to Cloud Front. This is done automatically for you when needed." self.conn_cloudfront = connect_cloudfront(self.AWS_ACCESS_KEY_ID, self.AWS_SECRET_ACCESS_KEY, debug=self.S3UTILS_DEBUG_LEVEL)
[ "def", "connect_cloudfront", "(", "self", ")", ":", "self", ".", "conn_cloudfront", "=", "connect_cloudfront", "(", "self", ".", "AWS_ACCESS_KEY_ID", ",", "self", ".", "AWS_SECRET_ACCESS_KEY", ",", "debug", "=", "self", ".", "S3UTILS_DEBUG_LEVEL", ")" ]
Connect to Cloud Front. This is done automatically for you when needed.
[ "Connect", "to", "Cloud", "Front", ".", "This", "is", "done", "automatically", "for", "you", "when", "needed", "." ]
aea41388a023dcf1e95588402077e31097514cf1
https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L166-L168
train
seperman/s3utils
s3utils/s3utils.py
S3utils.mkdir
def mkdir(self, target_folder): """ Create a folder on S3. Examples -------- >>> s3utils.mkdir("path/to/my_folder") Making directory: path/to/my_folder """ self.printv("Making directory: %s" % target_folder) self.k.key = re.sub(r"^/|/$", "", target_folder) + "/" self.k.set_contents_from_string('') self.k.close()
python
def mkdir(self, target_folder): """ Create a folder on S3. Examples -------- >>> s3utils.mkdir("path/to/my_folder") Making directory: path/to/my_folder """ self.printv("Making directory: %s" % target_folder) self.k.key = re.sub(r"^/|/$", "", target_folder) + "/" self.k.set_contents_from_string('') self.k.close()
[ "def", "mkdir", "(", "self", ",", "target_folder", ")", ":", "self", ".", "printv", "(", "\"Making directory: %s\"", "%", "target_folder", ")", "self", ".", "k", ".", "key", "=", "re", ".", "sub", "(", "r\"^/|/$\"", ",", "\"\"", ",", "target_folder", ")", "+", "\"/\"", "self", ".", "k", ".", "set_contents_from_string", "(", "''", ")", "self", ".", "k", ".", "close", "(", ")" ]
Create a folder on S3. Examples -------- >>> s3utils.mkdir("path/to/my_folder") Making directory: path/to/my_folder
[ "Create", "a", "folder", "on", "S3", "." ]
aea41388a023dcf1e95588402077e31097514cf1
https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L171-L183
train
seperman/s3utils
s3utils/s3utils.py
S3utils.rm
def rm(self, path): """ Delete the path and anything under the path. Example ------- >>> s3utils.rm("path/to/file_or_folder") """ list_of_files = list(self.ls(path)) if list_of_files: if len(list_of_files) == 1: self.bucket.delete_key(list_of_files[0]) else: self.bucket.delete_keys(list_of_files) self.printv("Deleted: %s" % list_of_files) else: logger.error("There was nothing to remove under %s", path)
python
def rm(self, path): """ Delete the path and anything under the path. Example ------- >>> s3utils.rm("path/to/file_or_folder") """ list_of_files = list(self.ls(path)) if list_of_files: if len(list_of_files) == 1: self.bucket.delete_key(list_of_files[0]) else: self.bucket.delete_keys(list_of_files) self.printv("Deleted: %s" % list_of_files) else: logger.error("There was nothing to remove under %s", path)
[ "def", "rm", "(", "self", ",", "path", ")", ":", "list_of_files", "=", "list", "(", "self", ".", "ls", "(", "path", ")", ")", "if", "list_of_files", ":", "if", "len", "(", "list_of_files", ")", "==", "1", ":", "self", ".", "bucket", ".", "delete_key", "(", "list_of_files", "[", "0", "]", ")", "else", ":", "self", ".", "bucket", ".", "delete_keys", "(", "list_of_files", ")", "self", ".", "printv", "(", "\"Deleted: %s\"", "%", "list_of_files", ")", "else", ":", "logger", ".", "error", "(", "\"There was nothing to remove under %s\"", ",", "path", ")" ]
Delete the path and anything under the path. Example ------- >>> s3utils.rm("path/to/file_or_folder")
[ "Delete", "the", "path", "and", "anything", "under", "the", "path", "." ]
aea41388a023dcf1e95588402077e31097514cf1
https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L186-L204
train
seperman/s3utils
s3utils/s3utils.py
S3utils.__put_key
def __put_key(self, local_file, target_file, acl='public-read', del_after_upload=False, overwrite=True, source="filename"): """Copy a file to s3.""" action_word = "moving" if del_after_upload else "copying" try: self.k.key = target_file # setting the path (key) of file in the container if source == "filename": # grabs the contents from local_file address. Note that it loads the whole file into memory self.k.set_contents_from_filename(local_file, self.AWS_HEADERS) elif source == "fileobj": self.k.set_contents_from_file(local_file, self.AWS_HEADERS) elif source == "string": self.k.set_contents_from_string(local_file, self.AWS_HEADERS) else: raise Exception("%s is not implemented as a source." % source) self.k.set_acl(acl) # setting the file permissions self.k.close() # not sure if it is needed. Somewhere I read it is recommended. self.printv("%s %s to %s" % (action_word, local_file, target_file)) # if it is supposed to delete the local file after uploading if del_after_upload and source == "filename": try: os.remove(local_file) except: logger.error("Unable to delete the file: ", local_file, exc_info=True) return True except: logger.error("Error in writing to %s", target_file, exc_info=True) return False
python
def __put_key(self, local_file, target_file, acl='public-read', del_after_upload=False, overwrite=True, source="filename"): """Copy a file to s3.""" action_word = "moving" if del_after_upload else "copying" try: self.k.key = target_file # setting the path (key) of file in the container if source == "filename": # grabs the contents from local_file address. Note that it loads the whole file into memory self.k.set_contents_from_filename(local_file, self.AWS_HEADERS) elif source == "fileobj": self.k.set_contents_from_file(local_file, self.AWS_HEADERS) elif source == "string": self.k.set_contents_from_string(local_file, self.AWS_HEADERS) else: raise Exception("%s is not implemented as a source." % source) self.k.set_acl(acl) # setting the file permissions self.k.close() # not sure if it is needed. Somewhere I read it is recommended. self.printv("%s %s to %s" % (action_word, local_file, target_file)) # if it is supposed to delete the local file after uploading if del_after_upload and source == "filename": try: os.remove(local_file) except: logger.error("Unable to delete the file: ", local_file, exc_info=True) return True except: logger.error("Error in writing to %s", target_file, exc_info=True) return False
[ "def", "__put_key", "(", "self", ",", "local_file", ",", "target_file", ",", "acl", "=", "'public-read'", ",", "del_after_upload", "=", "False", ",", "overwrite", "=", "True", ",", "source", "=", "\"filename\"", ")", ":", "action_word", "=", "\"moving\"", "if", "del_after_upload", "else", "\"copying\"", "try", ":", "self", ".", "k", ".", "key", "=", "target_file", "# setting the path (key) of file in the container", "if", "source", "==", "\"filename\"", ":", "# grabs the contents from local_file address. Note that it loads the whole file into memory", "self", ".", "k", ".", "set_contents_from_filename", "(", "local_file", ",", "self", ".", "AWS_HEADERS", ")", "elif", "source", "==", "\"fileobj\"", ":", "self", ".", "k", ".", "set_contents_from_file", "(", "local_file", ",", "self", ".", "AWS_HEADERS", ")", "elif", "source", "==", "\"string\"", ":", "self", ".", "k", ".", "set_contents_from_string", "(", "local_file", ",", "self", ".", "AWS_HEADERS", ")", "else", ":", "raise", "Exception", "(", "\"%s is not implemented as a source.\"", "%", "source", ")", "self", ".", "k", ".", "set_acl", "(", "acl", ")", "# setting the file permissions", "self", ".", "k", ".", "close", "(", ")", "# not sure if it is needed. Somewhere I read it is recommended.", "self", ".", "printv", "(", "\"%s %s to %s\"", "%", "(", "action_word", ",", "local_file", ",", "target_file", ")", ")", "# if it is supposed to delete the local file after uploading", "if", "del_after_upload", "and", "source", "==", "\"filename\"", ":", "try", ":", "os", ".", "remove", "(", "local_file", ")", "except", ":", "logger", ".", "error", "(", "\"Unable to delete the file: \"", ",", "local_file", ",", "exc_info", "=", "True", ")", "return", "True", "except", ":", "logger", ".", "error", "(", "\"Error in writing to %s\"", ",", "target_file", ",", "exc_info", "=", "True", ")", "return", "False" ]
Copy a file to s3.
[ "Copy", "a", "file", "to", "s3", "." ]
aea41388a023dcf1e95588402077e31097514cf1
https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L207-L238
train
seperman/s3utils
s3utils/s3utils.py
S3utils.cp
def cp(self, local_path, target_path, acl='public-read', del_after_upload=False, overwrite=True, invalidate=False): """ Copy a file or folder from local to s3. Parameters ---------- local_path : string Path to file or folder. Or if you want to copy only the contents of folder, add /* at the end of folder name target_path : string Target path on S3 bucket. acl : string, optional File permissions on S3. Default is public-read options: - private: Owner gets FULL_CONTROL. No one else has any access rights. - public-read: Owners gets FULL_CONTROL and the anonymous principal is granted READ access. - public-read-write: Owner gets FULL_CONTROL and the anonymous principal is granted READ and WRITE access. - authenticated-read: Owner gets FULL_CONTROL and any principal authenticated as a registered Amazon S3 user is granted READ access del_after_upload : boolean, optional delete the local file after uploading. This is effectively like moving the file. You can use s3utils.mv instead of s3utils.cp to move files from local to S3. It basically sets this flag to True. default = False overwrite : boolean, optional overwrites files on S3 if set to True. Default is True invalidate : boolean, optional invalidates the CDN (a.k.a Distribution) cache if the file already exists on S3 default = False Note that invalidation might take up to 15 minutes to take place. It is easier and faster to use cache buster to grab lastest version of your file on CDN than invalidation. **Returns** Nothing on success but it will return what went wrong if something fails. Examples -------- >>> s3utils.cp("path/to/folder","/test/") copying /path/to/myfolder/test2.txt to test/myfolder/test2.txt copying /path/to/myfolder/test.txt to test/myfolder/test.txt copying /path/to/myfolder/hoho/photo.JPG to test/myfolder/hoho/photo.JPG copying /path/to/myfolder/hoho/haha/ff to test/myfolder/hoho/haha/ff >>> # When overwrite is set to False, it returns the file(s) that were already existing on s3 and were not overwritten. >>> s3utils.cp("/tmp/test3.txt", "test3.txt", overwrite=False) ERROR:root:test3.txt already exist. Not overwriting. >>> {'existing_files': {'test3.txt'}} >>> # To overwrite the files on S3 and invalidate the CDN (cloudfront) cache so the new file goes on CDN: >>> s3utils.cp("path/to/folder","/test/", invalidate=True) copying /path/to/myfolder/test2.txt to test/myfolder/test2.txt copying /path/to/myfolder/test.txt to test/myfolder/test.txt copying /path/to/myfolder/hoho/photo.JPG to test/myfolder/hoho/photo.JPG copying /path/to/myfolder/hoho/haha/ff to test/myfolder/hoho/haha/ff >>> # When file does not exist, it returns a dictionary of what went wrong. >>> s3utils.cp("/tmp/does_not_exist", "somewhere") ERROR:root:trying to upload to s3 but file doesn't exist: /tmp/does_not_exist >>> {'file_does_not_exist': '/tmp/does_not_exist'} """ result = None if overwrite: list_of_files = [] else: list_of_files = self.ls(folder=target_path, begin_from_file="", num=-1, get_grants=False, all_grant_data=False) # copying the contents of the folder and not folder itself if local_path.endswith("/*"): local_path = local_path[:-2] target_path = re.sub(r"^/|/$", "", target_path) # Amazon S3 doesn't let the name to begin with / # copying folder too else: local_base_name = os.path.basename(local_path) local_path = re.sub(r"/$", "", local_path) target_path = re.sub(r"^/", "", target_path) if not target_path.endswith(local_base_name): target_path = os.path.join(target_path, local_base_name) if os.path.exists(local_path): result = self.__find_files_and_copy(local_path, target_path, acl, del_after_upload, overwrite, invalidate, list_of_files) else: result = {'file_does_not_exist': local_path} logger.error("trying to upload to s3 but file doesn't exist: %s" % local_path) return result
python
def cp(self, local_path, target_path, acl='public-read', del_after_upload=False, overwrite=True, invalidate=False): """ Copy a file or folder from local to s3. Parameters ---------- local_path : string Path to file or folder. Or if you want to copy only the contents of folder, add /* at the end of folder name target_path : string Target path on S3 bucket. acl : string, optional File permissions on S3. Default is public-read options: - private: Owner gets FULL_CONTROL. No one else has any access rights. - public-read: Owners gets FULL_CONTROL and the anonymous principal is granted READ access. - public-read-write: Owner gets FULL_CONTROL and the anonymous principal is granted READ and WRITE access. - authenticated-read: Owner gets FULL_CONTROL and any principal authenticated as a registered Amazon S3 user is granted READ access del_after_upload : boolean, optional delete the local file after uploading. This is effectively like moving the file. You can use s3utils.mv instead of s3utils.cp to move files from local to S3. It basically sets this flag to True. default = False overwrite : boolean, optional overwrites files on S3 if set to True. Default is True invalidate : boolean, optional invalidates the CDN (a.k.a Distribution) cache if the file already exists on S3 default = False Note that invalidation might take up to 15 minutes to take place. It is easier and faster to use cache buster to grab lastest version of your file on CDN than invalidation. **Returns** Nothing on success but it will return what went wrong if something fails. Examples -------- >>> s3utils.cp("path/to/folder","/test/") copying /path/to/myfolder/test2.txt to test/myfolder/test2.txt copying /path/to/myfolder/test.txt to test/myfolder/test.txt copying /path/to/myfolder/hoho/photo.JPG to test/myfolder/hoho/photo.JPG copying /path/to/myfolder/hoho/haha/ff to test/myfolder/hoho/haha/ff >>> # When overwrite is set to False, it returns the file(s) that were already existing on s3 and were not overwritten. >>> s3utils.cp("/tmp/test3.txt", "test3.txt", overwrite=False) ERROR:root:test3.txt already exist. Not overwriting. >>> {'existing_files': {'test3.txt'}} >>> # To overwrite the files on S3 and invalidate the CDN (cloudfront) cache so the new file goes on CDN: >>> s3utils.cp("path/to/folder","/test/", invalidate=True) copying /path/to/myfolder/test2.txt to test/myfolder/test2.txt copying /path/to/myfolder/test.txt to test/myfolder/test.txt copying /path/to/myfolder/hoho/photo.JPG to test/myfolder/hoho/photo.JPG copying /path/to/myfolder/hoho/haha/ff to test/myfolder/hoho/haha/ff >>> # When file does not exist, it returns a dictionary of what went wrong. >>> s3utils.cp("/tmp/does_not_exist", "somewhere") ERROR:root:trying to upload to s3 but file doesn't exist: /tmp/does_not_exist >>> {'file_does_not_exist': '/tmp/does_not_exist'} """ result = None if overwrite: list_of_files = [] else: list_of_files = self.ls(folder=target_path, begin_from_file="", num=-1, get_grants=False, all_grant_data=False) # copying the contents of the folder and not folder itself if local_path.endswith("/*"): local_path = local_path[:-2] target_path = re.sub(r"^/|/$", "", target_path) # Amazon S3 doesn't let the name to begin with / # copying folder too else: local_base_name = os.path.basename(local_path) local_path = re.sub(r"/$", "", local_path) target_path = re.sub(r"^/", "", target_path) if not target_path.endswith(local_base_name): target_path = os.path.join(target_path, local_base_name) if os.path.exists(local_path): result = self.__find_files_and_copy(local_path, target_path, acl, del_after_upload, overwrite, invalidate, list_of_files) else: result = {'file_does_not_exist': local_path} logger.error("trying to upload to s3 but file doesn't exist: %s" % local_path) return result
[ "def", "cp", "(", "self", ",", "local_path", ",", "target_path", ",", "acl", "=", "'public-read'", ",", "del_after_upload", "=", "False", ",", "overwrite", "=", "True", ",", "invalidate", "=", "False", ")", ":", "result", "=", "None", "if", "overwrite", ":", "list_of_files", "=", "[", "]", "else", ":", "list_of_files", "=", "self", ".", "ls", "(", "folder", "=", "target_path", ",", "begin_from_file", "=", "\"\"", ",", "num", "=", "-", "1", ",", "get_grants", "=", "False", ",", "all_grant_data", "=", "False", ")", "# copying the contents of the folder and not folder itself", "if", "local_path", ".", "endswith", "(", "\"/*\"", ")", ":", "local_path", "=", "local_path", "[", ":", "-", "2", "]", "target_path", "=", "re", ".", "sub", "(", "r\"^/|/$\"", ",", "\"\"", ",", "target_path", ")", "# Amazon S3 doesn't let the name to begin with /", "# copying folder too", "else", ":", "local_base_name", "=", "os", ".", "path", ".", "basename", "(", "local_path", ")", "local_path", "=", "re", ".", "sub", "(", "r\"/$\"", ",", "\"\"", ",", "local_path", ")", "target_path", "=", "re", ".", "sub", "(", "r\"^/\"", ",", "\"\"", ",", "target_path", ")", "if", "not", "target_path", ".", "endswith", "(", "local_base_name", ")", ":", "target_path", "=", "os", ".", "path", ".", "join", "(", "target_path", ",", "local_base_name", ")", "if", "os", ".", "path", ".", "exists", "(", "local_path", ")", ":", "result", "=", "self", ".", "__find_files_and_copy", "(", "local_path", ",", "target_path", ",", "acl", ",", "del_after_upload", ",", "overwrite", ",", "invalidate", ",", "list_of_files", ")", "else", ":", "result", "=", "{", "'file_does_not_exist'", ":", "local_path", "}", "logger", ".", "error", "(", "\"trying to upload to s3 but file doesn't exist: %s\"", "%", "local_path", ")", "return", "result" ]
Copy a file or folder from local to s3. Parameters ---------- local_path : string Path to file or folder. Or if you want to copy only the contents of folder, add /* at the end of folder name target_path : string Target path on S3 bucket. acl : string, optional File permissions on S3. Default is public-read options: - private: Owner gets FULL_CONTROL. No one else has any access rights. - public-read: Owners gets FULL_CONTROL and the anonymous principal is granted READ access. - public-read-write: Owner gets FULL_CONTROL and the anonymous principal is granted READ and WRITE access. - authenticated-read: Owner gets FULL_CONTROL and any principal authenticated as a registered Amazon S3 user is granted READ access del_after_upload : boolean, optional delete the local file after uploading. This is effectively like moving the file. You can use s3utils.mv instead of s3utils.cp to move files from local to S3. It basically sets this flag to True. default = False overwrite : boolean, optional overwrites files on S3 if set to True. Default is True invalidate : boolean, optional invalidates the CDN (a.k.a Distribution) cache if the file already exists on S3 default = False Note that invalidation might take up to 15 minutes to take place. It is easier and faster to use cache buster to grab lastest version of your file on CDN than invalidation. **Returns** Nothing on success but it will return what went wrong if something fails. Examples -------- >>> s3utils.cp("path/to/folder","/test/") copying /path/to/myfolder/test2.txt to test/myfolder/test2.txt copying /path/to/myfolder/test.txt to test/myfolder/test.txt copying /path/to/myfolder/hoho/photo.JPG to test/myfolder/hoho/photo.JPG copying /path/to/myfolder/hoho/haha/ff to test/myfolder/hoho/haha/ff >>> # When overwrite is set to False, it returns the file(s) that were already existing on s3 and were not overwritten. >>> s3utils.cp("/tmp/test3.txt", "test3.txt", overwrite=False) ERROR:root:test3.txt already exist. Not overwriting. >>> {'existing_files': {'test3.txt'}} >>> # To overwrite the files on S3 and invalidate the CDN (cloudfront) cache so the new file goes on CDN: >>> s3utils.cp("path/to/folder","/test/", invalidate=True) copying /path/to/myfolder/test2.txt to test/myfolder/test2.txt copying /path/to/myfolder/test.txt to test/myfolder/test.txt copying /path/to/myfolder/hoho/photo.JPG to test/myfolder/hoho/photo.JPG copying /path/to/myfolder/hoho/haha/ff to test/myfolder/hoho/haha/ff >>> # When file does not exist, it returns a dictionary of what went wrong. >>> s3utils.cp("/tmp/does_not_exist", "somewhere") ERROR:root:trying to upload to s3 but file doesn't exist: /tmp/does_not_exist >>> {'file_does_not_exist': '/tmp/does_not_exist'}
[ "Copy", "a", "file", "or", "folder", "from", "local", "to", "s3", "." ]
aea41388a023dcf1e95588402077e31097514cf1
https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L240-L336
train
seperman/s3utils
s3utils/s3utils.py
S3utils.mv
def mv(self, local_file, target_file, acl='public-read', overwrite=True, invalidate=False): """ Similar to Linux mv command. Move the file to the S3 and deletes the local copy It is basically s3utils.cp that has del_after_upload=True Examples -------- >>> s3utils.mv("path/to/folder","/test/") moving /path/to/myfolder/test2.txt to test/myfolder/test2.txt moving /path/to/myfolder/test.txt to test/myfolder/test.txt moving /path/to/myfolder/hoho/photo.JPG to test/myfolder/hoho/photo.JPG moving /path/to/myfolder/hoho/haha/ff to test/myfolder/hoho/haha/ff **Returns:** Nothing on success, otherwise what went wrong. Return type: dict """ self.cp(local_file, target_file, acl=acl, del_after_upload=True, overwrite=overwrite, invalidate=invalidate)
python
def mv(self, local_file, target_file, acl='public-read', overwrite=True, invalidate=False): """ Similar to Linux mv command. Move the file to the S3 and deletes the local copy It is basically s3utils.cp that has del_after_upload=True Examples -------- >>> s3utils.mv("path/to/folder","/test/") moving /path/to/myfolder/test2.txt to test/myfolder/test2.txt moving /path/to/myfolder/test.txt to test/myfolder/test.txt moving /path/to/myfolder/hoho/photo.JPG to test/myfolder/hoho/photo.JPG moving /path/to/myfolder/hoho/haha/ff to test/myfolder/hoho/haha/ff **Returns:** Nothing on success, otherwise what went wrong. Return type: dict """ self.cp(local_file, target_file, acl=acl, del_after_upload=True, overwrite=overwrite, invalidate=invalidate)
[ "def", "mv", "(", "self", ",", "local_file", ",", "target_file", ",", "acl", "=", "'public-read'", ",", "overwrite", "=", "True", ",", "invalidate", "=", "False", ")", ":", "self", ".", "cp", "(", "local_file", ",", "target_file", ",", "acl", "=", "acl", ",", "del_after_upload", "=", "True", ",", "overwrite", "=", "overwrite", ",", "invalidate", "=", "invalidate", ")" ]
Similar to Linux mv command. Move the file to the S3 and deletes the local copy It is basically s3utils.cp that has del_after_upload=True Examples -------- >>> s3utils.mv("path/to/folder","/test/") moving /path/to/myfolder/test2.txt to test/myfolder/test2.txt moving /path/to/myfolder/test.txt to test/myfolder/test.txt moving /path/to/myfolder/hoho/photo.JPG to test/myfolder/hoho/photo.JPG moving /path/to/myfolder/hoho/haha/ff to test/myfolder/hoho/haha/ff **Returns:** Nothing on success, otherwise what went wrong. Return type: dict
[ "Similar", "to", "Linux", "mv", "command", "." ]
aea41388a023dcf1e95588402077e31097514cf1
https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L483-L507
train
seperman/s3utils
s3utils/s3utils.py
S3utils.cp_cropduster_image
def cp_cropduster_image(self, the_image_path, del_after_upload=False, overwrite=False, invalidate=False): """ Deal with saving cropduster images to S3. Cropduster is a Django library for resizing editorial images. S3utils was originally written to put cropduster images on S3 bucket. Extra Items in your Django Settings ----------------------------------- MEDIA_ROOT : string Django media root. Currently it is ONLY used in cp_cropduster_image method. NOT any other method as this library was originally made to put Django cropduster images on s3 bucket. S3_ROOT_BASE : string S3 media root base. This will be the root folder in S3. Currently it is ONLY used in cp_cropduster_image method. NOT any other method as this library was originally made to put Django cropduster images on s3 bucket. """ local_file = os.path.join(settings.MEDIA_ROOT, the_image_path) # only try to upload things if the origin cropduster file exists (so it is not already uploaded to the CDN) if os.path.exists(local_file): the_image_crops_path = os.path.splitext(the_image_path)[0] the_image_crops_path_full_path = os.path.join(settings.MEDIA_ROOT, the_image_crops_path) self.cp(local_path=local_file, target_path=os.path.join(settings.S3_ROOT_BASE, the_image_path), del_after_upload=del_after_upload, overwrite=overwrite, invalidate=invalidate, ) self.cp(local_path=the_image_crops_path_full_path + "/*", target_path=os.path.join(settings.S3_ROOT_BASE, the_image_crops_path), del_after_upload=del_after_upload, overwrite=overwrite, invalidate=invalidate, )
python
def cp_cropduster_image(self, the_image_path, del_after_upload=False, overwrite=False, invalidate=False): """ Deal with saving cropduster images to S3. Cropduster is a Django library for resizing editorial images. S3utils was originally written to put cropduster images on S3 bucket. Extra Items in your Django Settings ----------------------------------- MEDIA_ROOT : string Django media root. Currently it is ONLY used in cp_cropduster_image method. NOT any other method as this library was originally made to put Django cropduster images on s3 bucket. S3_ROOT_BASE : string S3 media root base. This will be the root folder in S3. Currently it is ONLY used in cp_cropduster_image method. NOT any other method as this library was originally made to put Django cropduster images on s3 bucket. """ local_file = os.path.join(settings.MEDIA_ROOT, the_image_path) # only try to upload things if the origin cropduster file exists (so it is not already uploaded to the CDN) if os.path.exists(local_file): the_image_crops_path = os.path.splitext(the_image_path)[0] the_image_crops_path_full_path = os.path.join(settings.MEDIA_ROOT, the_image_crops_path) self.cp(local_path=local_file, target_path=os.path.join(settings.S3_ROOT_BASE, the_image_path), del_after_upload=del_after_upload, overwrite=overwrite, invalidate=invalidate, ) self.cp(local_path=the_image_crops_path_full_path + "/*", target_path=os.path.join(settings.S3_ROOT_BASE, the_image_crops_path), del_after_upload=del_after_upload, overwrite=overwrite, invalidate=invalidate, )
[ "def", "cp_cropduster_image", "(", "self", ",", "the_image_path", ",", "del_after_upload", "=", "False", ",", "overwrite", "=", "False", ",", "invalidate", "=", "False", ")", ":", "local_file", "=", "os", ".", "path", ".", "join", "(", "settings", ".", "MEDIA_ROOT", ",", "the_image_path", ")", "# only try to upload things if the origin cropduster file exists (so it is not already uploaded to the CDN)", "if", "os", ".", "path", ".", "exists", "(", "local_file", ")", ":", "the_image_crops_path", "=", "os", ".", "path", ".", "splitext", "(", "the_image_path", ")", "[", "0", "]", "the_image_crops_path_full_path", "=", "os", ".", "path", ".", "join", "(", "settings", ".", "MEDIA_ROOT", ",", "the_image_crops_path", ")", "self", ".", "cp", "(", "local_path", "=", "local_file", ",", "target_path", "=", "os", ".", "path", ".", "join", "(", "settings", ".", "S3_ROOT_BASE", ",", "the_image_path", ")", ",", "del_after_upload", "=", "del_after_upload", ",", "overwrite", "=", "overwrite", ",", "invalidate", "=", "invalidate", ",", ")", "self", ".", "cp", "(", "local_path", "=", "the_image_crops_path_full_path", "+", "\"/*\"", ",", "target_path", "=", "os", ".", "path", ".", "join", "(", "settings", ".", "S3_ROOT_BASE", ",", "the_image_crops_path", ")", ",", "del_after_upload", "=", "del_after_upload", ",", "overwrite", "=", "overwrite", ",", "invalidate", "=", "invalidate", ",", ")" ]
Deal with saving cropduster images to S3. Cropduster is a Django library for resizing editorial images. S3utils was originally written to put cropduster images on S3 bucket. Extra Items in your Django Settings ----------------------------------- MEDIA_ROOT : string Django media root. Currently it is ONLY used in cp_cropduster_image method. NOT any other method as this library was originally made to put Django cropduster images on s3 bucket. S3_ROOT_BASE : string S3 media root base. This will be the root folder in S3. Currently it is ONLY used in cp_cropduster_image method. NOT any other method as this library was originally made to put Django cropduster images on s3 bucket.
[ "Deal", "with", "saving", "cropduster", "images", "to", "S3", ".", "Cropduster", "is", "a", "Django", "library", "for", "resizing", "editorial", "images", ".", "S3utils", "was", "originally", "written", "to", "put", "cropduster", "images", "on", "S3", "bucket", "." ]
aea41388a023dcf1e95588402077e31097514cf1
https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L510-L551
train
seperman/s3utils
s3utils/s3utils.py
S3utils.chmod
def chmod(self, target_file, acl='public-read'): """ sets permissions for a file on S3 Parameters ---------- target_file : string Path to file on S3 acl : string, optional File permissions on S3. Default is public-read options: - private: Owner gets FULL_CONTROL. No one else has any access rights. - public-read: Owners gets FULL_CONTROL and the anonymous principal is granted READ access. - public-read-write: Owner gets FULL_CONTROL and the anonymous principal is granted READ and WRITE access. - authenticated-read: Owner gets FULL_CONTROL and any principal authenticated as a registered Amazon S3 user is granted READ access Examples -------- >>> s3utils.chmod("path/to/file","private") """ self.k.key = target_file # setting the path (key) of file in the container self.k.set_acl(acl) # setting the file permissions self.k.close()
python
def chmod(self, target_file, acl='public-read'): """ sets permissions for a file on S3 Parameters ---------- target_file : string Path to file on S3 acl : string, optional File permissions on S3. Default is public-read options: - private: Owner gets FULL_CONTROL. No one else has any access rights. - public-read: Owners gets FULL_CONTROL and the anonymous principal is granted READ access. - public-read-write: Owner gets FULL_CONTROL and the anonymous principal is granted READ and WRITE access. - authenticated-read: Owner gets FULL_CONTROL and any principal authenticated as a registered Amazon S3 user is granted READ access Examples -------- >>> s3utils.chmod("path/to/file","private") """ self.k.key = target_file # setting the path (key) of file in the container self.k.set_acl(acl) # setting the file permissions self.k.close()
[ "def", "chmod", "(", "self", ",", "target_file", ",", "acl", "=", "'public-read'", ")", ":", "self", ".", "k", ".", "key", "=", "target_file", "# setting the path (key) of file in the container", "self", ".", "k", ".", "set_acl", "(", "acl", ")", "# setting the file permissions", "self", ".", "k", ".", "close", "(", ")" ]
sets permissions for a file on S3 Parameters ---------- target_file : string Path to file on S3 acl : string, optional File permissions on S3. Default is public-read options: - private: Owner gets FULL_CONTROL. No one else has any access rights. - public-read: Owners gets FULL_CONTROL and the anonymous principal is granted READ access. - public-read-write: Owner gets FULL_CONTROL and the anonymous principal is granted READ and WRITE access. - authenticated-read: Owner gets FULL_CONTROL and any principal authenticated as a registered Amazon S3 user is granted READ access Examples -------- >>> s3utils.chmod("path/to/file","private")
[ "sets", "permissions", "for", "a", "file", "on", "S3" ]
aea41388a023dcf1e95588402077e31097514cf1
https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L582-L610
train
seperman/s3utils
s3utils/s3utils.py
S3utils.ll
def ll(self, folder="", begin_from_file="", num=-1, all_grant_data=False): """ Get the list of files and permissions from S3. This is similar to LL (ls -lah) in Linux: List of files with permissions. Parameters ---------- folder : string Path to file on S3 num: integer, optional number of results to return, by default it returns all results. begin_from_file : string, optional which file to start from on S3. This is usedful in case you are iterating over lists of files and you need to page the result by starting listing from a certain file and fetching certain num (number) of files. all_grant_data : Boolean, optional More detailed file permission data will be returned. Examples -------- >>> from s3utils import S3utils >>> s3utils = S3utils( ... AWS_ACCESS_KEY_ID = 'your access key', ... AWS_SECRET_ACCESS_KEY = 'your secret key', ... AWS_STORAGE_BUCKET_NAME = 'your bucket name', ... S3UTILS_DEBUG_LEVEL = 1, #change it to 0 for less verbose ... ) >>> import json >>> # We use json.dumps to print the results more readable: >>> my_folder_stuff = s3utils.ll("/test/") >>> print(json.dumps(my_folder_stuff, indent=2)) { "test/myfolder/": [ { "name": "owner's name", "permission": "FULL_CONTROL" } ], "test/myfolder/em/": [ { "name": "owner's name", "permission": "FULL_CONTROL" } ], "test/myfolder/hoho/": [ { "name": "owner's name", "permission": "FULL_CONTROL" } ], "test/myfolder/hoho/.DS_Store": [ { "name": "owner's name", "permission": "FULL_CONTROL" }, { "name": null, "permission": "READ" } ], "test/myfolder/hoho/haha/": [ { "name": "owner's name", "permission": "FULL_CONTROL" } ], "test/myfolder/hoho/haha/ff": [ { "name": "owner's name", "permission": "FULL_CONTROL" }, { "name": null, "permission": "READ" } ], "test/myfolder/hoho/photo.JPG": [ { "name": "owner's name", "permission": "FULL_CONTROL" }, { "name": null, "permission": "READ" } ], } """ return self.ls(folder=folder, begin_from_file=begin_from_file, num=num, get_grants=True, all_grant_data=all_grant_data)
python
def ll(self, folder="", begin_from_file="", num=-1, all_grant_data=False): """ Get the list of files and permissions from S3. This is similar to LL (ls -lah) in Linux: List of files with permissions. Parameters ---------- folder : string Path to file on S3 num: integer, optional number of results to return, by default it returns all results. begin_from_file : string, optional which file to start from on S3. This is usedful in case you are iterating over lists of files and you need to page the result by starting listing from a certain file and fetching certain num (number) of files. all_grant_data : Boolean, optional More detailed file permission data will be returned. Examples -------- >>> from s3utils import S3utils >>> s3utils = S3utils( ... AWS_ACCESS_KEY_ID = 'your access key', ... AWS_SECRET_ACCESS_KEY = 'your secret key', ... AWS_STORAGE_BUCKET_NAME = 'your bucket name', ... S3UTILS_DEBUG_LEVEL = 1, #change it to 0 for less verbose ... ) >>> import json >>> # We use json.dumps to print the results more readable: >>> my_folder_stuff = s3utils.ll("/test/") >>> print(json.dumps(my_folder_stuff, indent=2)) { "test/myfolder/": [ { "name": "owner's name", "permission": "FULL_CONTROL" } ], "test/myfolder/em/": [ { "name": "owner's name", "permission": "FULL_CONTROL" } ], "test/myfolder/hoho/": [ { "name": "owner's name", "permission": "FULL_CONTROL" } ], "test/myfolder/hoho/.DS_Store": [ { "name": "owner's name", "permission": "FULL_CONTROL" }, { "name": null, "permission": "READ" } ], "test/myfolder/hoho/haha/": [ { "name": "owner's name", "permission": "FULL_CONTROL" } ], "test/myfolder/hoho/haha/ff": [ { "name": "owner's name", "permission": "FULL_CONTROL" }, { "name": null, "permission": "READ" } ], "test/myfolder/hoho/photo.JPG": [ { "name": "owner's name", "permission": "FULL_CONTROL" }, { "name": null, "permission": "READ" } ], } """ return self.ls(folder=folder, begin_from_file=begin_from_file, num=num, get_grants=True, all_grant_data=all_grant_data)
[ "def", "ll", "(", "self", ",", "folder", "=", "\"\"", ",", "begin_from_file", "=", "\"\"", ",", "num", "=", "-", "1", ",", "all_grant_data", "=", "False", ")", ":", "return", "self", ".", "ls", "(", "folder", "=", "folder", ",", "begin_from_file", "=", "begin_from_file", ",", "num", "=", "num", ",", "get_grants", "=", "True", ",", "all_grant_data", "=", "all_grant_data", ")" ]
Get the list of files and permissions from S3. This is similar to LL (ls -lah) in Linux: List of files with permissions. Parameters ---------- folder : string Path to file on S3 num: integer, optional number of results to return, by default it returns all results. begin_from_file : string, optional which file to start from on S3. This is usedful in case you are iterating over lists of files and you need to page the result by starting listing from a certain file and fetching certain num (number) of files. all_grant_data : Boolean, optional More detailed file permission data will be returned. Examples -------- >>> from s3utils import S3utils >>> s3utils = S3utils( ... AWS_ACCESS_KEY_ID = 'your access key', ... AWS_SECRET_ACCESS_KEY = 'your secret key', ... AWS_STORAGE_BUCKET_NAME = 'your bucket name', ... S3UTILS_DEBUG_LEVEL = 1, #change it to 0 for less verbose ... ) >>> import json >>> # We use json.dumps to print the results more readable: >>> my_folder_stuff = s3utils.ll("/test/") >>> print(json.dumps(my_folder_stuff, indent=2)) { "test/myfolder/": [ { "name": "owner's name", "permission": "FULL_CONTROL" } ], "test/myfolder/em/": [ { "name": "owner's name", "permission": "FULL_CONTROL" } ], "test/myfolder/hoho/": [ { "name": "owner's name", "permission": "FULL_CONTROL" } ], "test/myfolder/hoho/.DS_Store": [ { "name": "owner's name", "permission": "FULL_CONTROL" }, { "name": null, "permission": "READ" } ], "test/myfolder/hoho/haha/": [ { "name": "owner's name", "permission": "FULL_CONTROL" } ], "test/myfolder/hoho/haha/ff": [ { "name": "owner's name", "permission": "FULL_CONTROL" }, { "name": null, "permission": "READ" } ], "test/myfolder/hoho/photo.JPG": [ { "name": "owner's name", "permission": "FULL_CONTROL" }, { "name": null, "permission": "READ" } ], }
[ "Get", "the", "list", "of", "files", "and", "permissions", "from", "S3", "." ]
aea41388a023dcf1e95588402077e31097514cf1
https://github.com/seperman/s3utils/blob/aea41388a023dcf1e95588402077e31097514cf1/s3utils/s3utils.py#L669-L764
train
uktrade/directory-signature-auth
sigauth/helpers.py
get_path
def get_path(url): """ Get the path from a given url, including the querystring. Args: url (str) Returns: str """ url = urlsplit(url) path = url.path if url.query: path += "?{}".format(url.query) return path
python
def get_path(url): """ Get the path from a given url, including the querystring. Args: url (str) Returns: str """ url = urlsplit(url) path = url.path if url.query: path += "?{}".format(url.query) return path
[ "def", "get_path", "(", "url", ")", ":", "url", "=", "urlsplit", "(", "url", ")", "path", "=", "url", ".", "path", "if", "url", ".", "query", ":", "path", "+=", "\"?{}\"", ".", "format", "(", "url", ".", "query", ")", "return", "path" ]
Get the path from a given url, including the querystring. Args: url (str) Returns: str
[ "Get", "the", "path", "from", "a", "given", "url", "including", "the", "querystring", "." ]
1a1b1e887b25a938133d7bcc146d3fecf1079313
https://github.com/uktrade/directory-signature-auth/blob/1a1b1e887b25a938133d7bcc146d3fecf1079313/sigauth/helpers.py#L79-L94
train
vkruoso/receita-tools
receita/tools/build.py
Build.run
def run(self): """Reads data from disk and generates CSV files.""" # Try to create the directory if not os.path.exists(self.output): try: os.mkdir(self.output) except: print 'failed to create output directory %s' % self.output # Be sure it is a directory if not os.path.isdir(self.output): print 'invalid output directory %s' % self.output sys.exit(1) # Create the CSV handlers visitors = [ _CompaniesCSV(self.output), _ActivitiesCSV(self.output), _ActivitiesSeenCSV(self.output), _QSACSV(self.output), ] # Run by each company populating the CSV files for path in glob.glob(os.path.join(self.input, '*.json')): with open(path, 'r') as f: try: data = json.load(f, encoding='utf-8') except ValueError: continue for visitor in visitors: visitor.visit(data)
python
def run(self): """Reads data from disk and generates CSV files.""" # Try to create the directory if not os.path.exists(self.output): try: os.mkdir(self.output) except: print 'failed to create output directory %s' % self.output # Be sure it is a directory if not os.path.isdir(self.output): print 'invalid output directory %s' % self.output sys.exit(1) # Create the CSV handlers visitors = [ _CompaniesCSV(self.output), _ActivitiesCSV(self.output), _ActivitiesSeenCSV(self.output), _QSACSV(self.output), ] # Run by each company populating the CSV files for path in glob.glob(os.path.join(self.input, '*.json')): with open(path, 'r') as f: try: data = json.load(f, encoding='utf-8') except ValueError: continue for visitor in visitors: visitor.visit(data)
[ "def", "run", "(", "self", ")", ":", "# Try to create the directory", "if", "not", "os", ".", "path", ".", "exists", "(", "self", ".", "output", ")", ":", "try", ":", "os", ".", "mkdir", "(", "self", ".", "output", ")", "except", ":", "print", "'failed to create output directory %s'", "%", "self", ".", "output", "# Be sure it is a directory", "if", "not", "os", ".", "path", ".", "isdir", "(", "self", ".", "output", ")", ":", "print", "'invalid output directory %s'", "%", "self", ".", "output", "sys", ".", "exit", "(", "1", ")", "# Create the CSV handlers", "visitors", "=", "[", "_CompaniesCSV", "(", "self", ".", "output", ")", ",", "_ActivitiesCSV", "(", "self", ".", "output", ")", ",", "_ActivitiesSeenCSV", "(", "self", ".", "output", ")", ",", "_QSACSV", "(", "self", ".", "output", ")", ",", "]", "# Run by each company populating the CSV files", "for", "path", "in", "glob", ".", "glob", "(", "os", ".", "path", ".", "join", "(", "self", ".", "input", ",", "'*.json'", ")", ")", ":", "with", "open", "(", "path", ",", "'r'", ")", "as", "f", ":", "try", ":", "data", "=", "json", ".", "load", "(", "f", ",", "encoding", "=", "'utf-8'", ")", "except", "ValueError", ":", "continue", "for", "visitor", "in", "visitors", ":", "visitor", ".", "visit", "(", "data", ")" ]
Reads data from disk and generates CSV files.
[ "Reads", "data", "from", "disk", "and", "generates", "CSV", "files", "." ]
fd62a252c76541c9feac6470b9048b31348ffe86
https://github.com/vkruoso/receita-tools/blob/fd62a252c76541c9feac6470b9048b31348ffe86/receita/tools/build.py#L144-L175
train
marrow/mongo
marrow/mongo/core/index.py
Index.process_fields
def process_fields(self, fields): """Process a list of simple string field definitions and assign their order based on prefix.""" result = [] strip = ''.join(self.PREFIX_MAP) for field in fields: direction = self.PREFIX_MAP[''] if field[0] in self.PREFIX_MAP: direction = self.PREFIX_MAP[field[0]] field = field.lstrip(strip) result.append((field, direction)) return result
python
def process_fields(self, fields): """Process a list of simple string field definitions and assign their order based on prefix.""" result = [] strip = ''.join(self.PREFIX_MAP) for field in fields: direction = self.PREFIX_MAP[''] if field[0] in self.PREFIX_MAP: direction = self.PREFIX_MAP[field[0]] field = field.lstrip(strip) result.append((field, direction)) return result
[ "def", "process_fields", "(", "self", ",", "fields", ")", ":", "result", "=", "[", "]", "strip", "=", "''", ".", "join", "(", "self", ".", "PREFIX_MAP", ")", "for", "field", "in", "fields", ":", "direction", "=", "self", ".", "PREFIX_MAP", "[", "''", "]", "if", "field", "[", "0", "]", "in", "self", ".", "PREFIX_MAP", ":", "direction", "=", "self", ".", "PREFIX_MAP", "[", "field", "[", "0", "]", "]", "field", "=", "field", ".", "lstrip", "(", "strip", ")", "result", ".", "append", "(", "(", "field", ",", "direction", ")", ")", "return", "result" ]
Process a list of simple string field definitions and assign their order based on prefix.
[ "Process", "a", "list", "of", "simple", "string", "field", "definitions", "and", "assign", "their", "order", "based", "on", "prefix", "." ]
2066dc73e281b8a46cb5fc965267d6b8e1b18467
https://github.com/marrow/mongo/blob/2066dc73e281b8a46cb5fc965267d6b8e1b18467/marrow/mongo/core/index.py#L60-L75
train
svartalf/python-2gis
dgis/__init__.py
API.search_in_rubric
def search_in_rubric(self, **kwargs): """Firms search in rubric http://api.2gis.ru/doc/firms/searches/searchinrubric/ """ point = kwargs.pop('point', False) if point: kwargs['point'] = '%s,%s' % point bound = kwargs.pop('bound', False) if bound: kwargs['bound[point1]'] = bound[0] kwargs['bound[point2]'] = bound[1] filters = kwargs.pop('filters', False) if filters: for k, v in filters.items(): kwargs['filters[%s]' % k] = v return self._search_in_rubric(**kwargs)
python
def search_in_rubric(self, **kwargs): """Firms search in rubric http://api.2gis.ru/doc/firms/searches/searchinrubric/ """ point = kwargs.pop('point', False) if point: kwargs['point'] = '%s,%s' % point bound = kwargs.pop('bound', False) if bound: kwargs['bound[point1]'] = bound[0] kwargs['bound[point2]'] = bound[1] filters = kwargs.pop('filters', False) if filters: for k, v in filters.items(): kwargs['filters[%s]' % k] = v return self._search_in_rubric(**kwargs)
[ "def", "search_in_rubric", "(", "self", ",", "*", "*", "kwargs", ")", ":", "point", "=", "kwargs", ".", "pop", "(", "'point'", ",", "False", ")", "if", "point", ":", "kwargs", "[", "'point'", "]", "=", "'%s,%s'", "%", "point", "bound", "=", "kwargs", ".", "pop", "(", "'bound'", ",", "False", ")", "if", "bound", ":", "kwargs", "[", "'bound[point1]'", "]", "=", "bound", "[", "0", "]", "kwargs", "[", "'bound[point2]'", "]", "=", "bound", "[", "1", "]", "filters", "=", "kwargs", ".", "pop", "(", "'filters'", ",", "False", ")", "if", "filters", ":", "for", "k", ",", "v", "in", "filters", ".", "items", "(", ")", ":", "kwargs", "[", "'filters[%s]'", "%", "k", "]", "=", "v", "return", "self", ".", "_search_in_rubric", "(", "*", "*", "kwargs", ")" ]
Firms search in rubric http://api.2gis.ru/doc/firms/searches/searchinrubric/
[ "Firms", "search", "in", "rubric" ]
6eccd6073c99494b7abf20b38a5455cbd55d6420
https://github.com/svartalf/python-2gis/blob/6eccd6073c99494b7abf20b38a5455cbd55d6420/dgis/__init__.py#L89-L109
train
tonybaloney/retox
retox/ui.py
RetoxRefreshMixin.refresh
def refresh(self): ''' Refresh the list and the screen ''' self._screen.force_update() self._screen.refresh() self._update(1)
python
def refresh(self): ''' Refresh the list and the screen ''' self._screen.force_update() self._screen.refresh() self._update(1)
[ "def", "refresh", "(", "self", ")", ":", "self", ".", "_screen", ".", "force_update", "(", ")", "self", ".", "_screen", ".", "refresh", "(", ")", "self", ".", "_update", "(", "1", ")" ]
Refresh the list and the screen
[ "Refresh", "the", "list", "and", "the", "screen" ]
4635e31001d2ac083423f46766249ac8daca7c9c
https://github.com/tonybaloney/retox/blob/4635e31001d2ac083423f46766249ac8daca7c9c/retox/ui.py#L54-L60
train
tonybaloney/retox
retox/ui.py
VirtualEnvironmentFrame.start
def start(self, activity, action): ''' Mark an action as started :param activity: The virtualenv activity name :type activity: ``str`` :param action: The virtualenv action :type action: :class:`tox.session.Action` ''' try: self._start_action(activity, action) except ValueError: retox_log.debug("Could not find action %s in env %s" % (activity, self.name)) self.refresh()
python
def start(self, activity, action): ''' Mark an action as started :param activity: The virtualenv activity name :type activity: ``str`` :param action: The virtualenv action :type action: :class:`tox.session.Action` ''' try: self._start_action(activity, action) except ValueError: retox_log.debug("Could not find action %s in env %s" % (activity, self.name)) self.refresh()
[ "def", "start", "(", "self", ",", "activity", ",", "action", ")", ":", "try", ":", "self", ".", "_start_action", "(", "activity", ",", "action", ")", "except", "ValueError", ":", "retox_log", ".", "debug", "(", "\"Could not find action %s in env %s\"", "%", "(", "activity", ",", "self", ".", "name", ")", ")", "self", ".", "refresh", "(", ")" ]
Mark an action as started :param activity: The virtualenv activity name :type activity: ``str`` :param action: The virtualenv action :type action: :class:`tox.session.Action`
[ "Mark", "an", "action", "as", "started" ]
4635e31001d2ac083423f46766249ac8daca7c9c
https://github.com/tonybaloney/retox/blob/4635e31001d2ac083423f46766249ac8daca7c9c/retox/ui.py#L233-L247
train
tonybaloney/retox
retox/ui.py
VirtualEnvironmentFrame.stop
def stop(self, activity, action): ''' Mark a task as completed :param activity: The virtualenv activity name :type activity: ``str`` :param action: The virtualenv action :type action: :class:`tox.session.Action` ''' try: self._remove_running_action(activity, action) except ValueError: retox_log.debug("Could not find action %s in env %s" % (activity, self.name)) self._mark_action_completed(activity, action) self.refresh()
python
def stop(self, activity, action): ''' Mark a task as completed :param activity: The virtualenv activity name :type activity: ``str`` :param action: The virtualenv action :type action: :class:`tox.session.Action` ''' try: self._remove_running_action(activity, action) except ValueError: retox_log.debug("Could not find action %s in env %s" % (activity, self.name)) self._mark_action_completed(activity, action) self.refresh()
[ "def", "stop", "(", "self", ",", "activity", ",", "action", ")", ":", "try", ":", "self", ".", "_remove_running_action", "(", "activity", ",", "action", ")", "except", "ValueError", ":", "retox_log", ".", "debug", "(", "\"Could not find action %s in env %s\"", "%", "(", "activity", ",", "self", ".", "name", ")", ")", "self", ".", "_mark_action_completed", "(", "activity", ",", "action", ")", "self", ".", "refresh", "(", ")" ]
Mark a task as completed :param activity: The virtualenv activity name :type activity: ``str`` :param action: The virtualenv action :type action: :class:`tox.session.Action`
[ "Mark", "a", "task", "as", "completed" ]
4635e31001d2ac083423f46766249ac8daca7c9c
https://github.com/tonybaloney/retox/blob/4635e31001d2ac083423f46766249ac8daca7c9c/retox/ui.py#L249-L264
train
tonybaloney/retox
retox/ui.py
VirtualEnvironmentFrame.finish
def finish(self, status): ''' Move laggard tasks over :param activity: The virtualenv status :type activity: ``str`` ''' retox_log.info("Completing %s with status %s" % (self.name, status)) result = Screen.COLOUR_GREEN if not status else Screen.COLOUR_RED self.palette['title'] = (Screen.COLOUR_WHITE, Screen.A_BOLD, result) for item in list(self._task_view.options): self._task_view.options.remove(item) self._completed_view.options.append(item) self.refresh()
python
def finish(self, status): ''' Move laggard tasks over :param activity: The virtualenv status :type activity: ``str`` ''' retox_log.info("Completing %s with status %s" % (self.name, status)) result = Screen.COLOUR_GREEN if not status else Screen.COLOUR_RED self.palette['title'] = (Screen.COLOUR_WHITE, Screen.A_BOLD, result) for item in list(self._task_view.options): self._task_view.options.remove(item) self._completed_view.options.append(item) self.refresh()
[ "def", "finish", "(", "self", ",", "status", ")", ":", "retox_log", ".", "info", "(", "\"Completing %s with status %s\"", "%", "(", "self", ".", "name", ",", "status", ")", ")", "result", "=", "Screen", ".", "COLOUR_GREEN", "if", "not", "status", "else", "Screen", ".", "COLOUR_RED", "self", ".", "palette", "[", "'title'", "]", "=", "(", "Screen", ".", "COLOUR_WHITE", ",", "Screen", ".", "A_BOLD", ",", "result", ")", "for", "item", "in", "list", "(", "self", ".", "_task_view", ".", "options", ")", ":", "self", ".", "_task_view", ".", "options", ".", "remove", "(", "item", ")", "self", ".", "_completed_view", ".", "options", ".", "append", "(", "item", ")", "self", ".", "refresh", "(", ")" ]
Move laggard tasks over :param activity: The virtualenv status :type activity: ``str``
[ "Move", "laggard", "tasks", "over" ]
4635e31001d2ac083423f46766249ac8daca7c9c
https://github.com/tonybaloney/retox/blob/4635e31001d2ac083423f46766249ac8daca7c9c/retox/ui.py#L266-L279
train
tonybaloney/retox
retox/ui.py
VirtualEnvironmentFrame.reset
def reset(self): ''' Reset the frame between jobs ''' self.palette['title'] = (Screen.COLOUR_WHITE, Screen.A_BOLD, Screen.COLOUR_BLUE) self._completed_view.options = [] self._task_view.options = [] self.refresh()
python
def reset(self): ''' Reset the frame between jobs ''' self.palette['title'] = (Screen.COLOUR_WHITE, Screen.A_BOLD, Screen.COLOUR_BLUE) self._completed_view.options = [] self._task_view.options = [] self.refresh()
[ "def", "reset", "(", "self", ")", ":", "self", ".", "palette", "[", "'title'", "]", "=", "(", "Screen", ".", "COLOUR_WHITE", ",", "Screen", ".", "A_BOLD", ",", "Screen", ".", "COLOUR_BLUE", ")", "self", ".", "_completed_view", ".", "options", "=", "[", "]", "self", ".", "_task_view", ".", "options", "=", "[", "]", "self", ".", "refresh", "(", ")" ]
Reset the frame between jobs
[ "Reset", "the", "frame", "between", "jobs" ]
4635e31001d2ac083423f46766249ac8daca7c9c
https://github.com/tonybaloney/retox/blob/4635e31001d2ac083423f46766249ac8daca7c9c/retox/ui.py#L281-L288
train
ryukinix/decorating
decorating/decorator.py
Decorator.default_arguments
def default_arguments(cls): """Returns the available kwargs of the called class""" func = cls.__init__ args = func.__code__.co_varnames defaults = func.__defaults__ index = -len(defaults) return {k: v for k, v in zip(args[index:], defaults)}
python
def default_arguments(cls): """Returns the available kwargs of the called class""" func = cls.__init__ args = func.__code__.co_varnames defaults = func.__defaults__ index = -len(defaults) return {k: v for k, v in zip(args[index:], defaults)}
[ "def", "default_arguments", "(", "cls", ")", ":", "func", "=", "cls", ".", "__init__", "args", "=", "func", ".", "__code__", ".", "co_varnames", "defaults", "=", "func", ".", "__defaults__", "index", "=", "-", "len", "(", "defaults", ")", "return", "{", "k", ":", "v", "for", "k", ",", "v", "in", "zip", "(", "args", "[", "index", ":", "]", ",", "defaults", ")", "}" ]
Returns the available kwargs of the called class
[ "Returns", "the", "available", "kwargs", "of", "the", "called", "class" ]
df78c3f87800205701704c0bc0fb9b6bb908ba7e
https://github.com/ryukinix/decorating/blob/df78c3f87800205701704c0bc0fb9b6bb908ba7e/decorating/decorator.py#L134-L140
train
ryukinix/decorating
decorating/decorator.py
Decorator.recreate
def recreate(cls, *args, **kwargs): """Recreate the class based in your args, multiple uses""" cls.check_arguments(kwargs) first_is_callable = True if any(args) and callable(args[0]) else False signature = cls.default_arguments() allowed_arguments = {k: v for k, v in kwargs.items() if k in signature} if (any(allowed_arguments) or any(args)) and not first_is_callable: if any(args) and not first_is_callable: return cls(args[0], **allowed_arguments) elif any(allowed_arguments): return cls(**allowed_arguments) return cls.instances[-1] if any(cls.instances) else cls()
python
def recreate(cls, *args, **kwargs): """Recreate the class based in your args, multiple uses""" cls.check_arguments(kwargs) first_is_callable = True if any(args) and callable(args[0]) else False signature = cls.default_arguments() allowed_arguments = {k: v for k, v in kwargs.items() if k in signature} if (any(allowed_arguments) or any(args)) and not first_is_callable: if any(args) and not first_is_callable: return cls(args[0], **allowed_arguments) elif any(allowed_arguments): return cls(**allowed_arguments) return cls.instances[-1] if any(cls.instances) else cls()
[ "def", "recreate", "(", "cls", ",", "*", "args", ",", "*", "*", "kwargs", ")", ":", "cls", ".", "check_arguments", "(", "kwargs", ")", "first_is_callable", "=", "True", "if", "any", "(", "args", ")", "and", "callable", "(", "args", "[", "0", "]", ")", "else", "False", "signature", "=", "cls", ".", "default_arguments", "(", ")", "allowed_arguments", "=", "{", "k", ":", "v", "for", "k", ",", "v", "in", "kwargs", ".", "items", "(", ")", "if", "k", "in", "signature", "}", "if", "(", "any", "(", "allowed_arguments", ")", "or", "any", "(", "args", ")", ")", "and", "not", "first_is_callable", ":", "if", "any", "(", "args", ")", "and", "not", "first_is_callable", ":", "return", "cls", "(", "args", "[", "0", "]", ",", "*", "*", "allowed_arguments", ")", "elif", "any", "(", "allowed_arguments", ")", ":", "return", "cls", "(", "*", "*", "allowed_arguments", ")", "return", "cls", ".", "instances", "[", "-", "1", "]", "if", "any", "(", "cls", ".", "instances", ")", "else", "cls", "(", ")" ]
Recreate the class based in your args, multiple uses
[ "Recreate", "the", "class", "based", "in", "your", "args", "multiple", "uses" ]
df78c3f87800205701704c0bc0fb9b6bb908ba7e
https://github.com/ryukinix/decorating/blob/df78c3f87800205701704c0bc0fb9b6bb908ba7e/decorating/decorator.py#L143-L155
train
ryukinix/decorating
decorating/decorator.py
Decorator.check_arguments
def check_arguments(cls, passed): """Put warnings of arguments whose can't be handle by the class""" defaults = list(cls.default_arguments().keys()) template = ("Pass arg {argument:!r} in {cname:!r}, can be a typo? " "Supported key arguments: {defaults}") fails = [] for arg in passed: if arg not in defaults: warn(template.format(argument=arg, cname=cls.__name__, defaults=defaults)) fails.append(arg) return any(fails)
python
def check_arguments(cls, passed): """Put warnings of arguments whose can't be handle by the class""" defaults = list(cls.default_arguments().keys()) template = ("Pass arg {argument:!r} in {cname:!r}, can be a typo? " "Supported key arguments: {defaults}") fails = [] for arg in passed: if arg not in defaults: warn(template.format(argument=arg, cname=cls.__name__, defaults=defaults)) fails.append(arg) return any(fails)
[ "def", "check_arguments", "(", "cls", ",", "passed", ")", ":", "defaults", "=", "list", "(", "cls", ".", "default_arguments", "(", ")", ".", "keys", "(", ")", ")", "template", "=", "(", "\"Pass arg {argument:!r} in {cname:!r}, can be a typo? \"", "\"Supported key arguments: {defaults}\"", ")", "fails", "=", "[", "]", "for", "arg", "in", "passed", ":", "if", "arg", "not", "in", "defaults", ":", "warn", "(", "template", ".", "format", "(", "argument", "=", "arg", ",", "cname", "=", "cls", ".", "__name__", ",", "defaults", "=", "defaults", ")", ")", "fails", ".", "append", "(", "arg", ")", "return", "any", "(", "fails", ")" ]
Put warnings of arguments whose can't be handle by the class
[ "Put", "warnings", "of", "arguments", "whose", "can", "t", "be", "handle", "by", "the", "class" ]
df78c3f87800205701704c0bc0fb9b6bb908ba7e
https://github.com/ryukinix/decorating/blob/df78c3f87800205701704c0bc0fb9b6bb908ba7e/decorating/decorator.py#L158-L171
train
ovnicraft/suds2
suds/builder.py
Builder.process
def process(self, data, type, history): """ process the specified type then process its children """ if type in history: return if type.enum(): return history.append(type) resolved = type.resolve() value = None if type.multi_occurrence(): value = [] else: if len(resolved) > 0: if resolved.mixed(): value = Factory.property(resolved.name) md = value.__metadata__ md.sxtype = resolved else: value = Factory.object(resolved.name) md = value.__metadata__ md.sxtype = resolved md.ordering = self.ordering(resolved) setattr(data, type.name, value) if value is not None: data = value if not isinstance(data, list): self.add_attributes(data, resolved) for child, ancestry in resolved.children(): if self.skip_child(child, ancestry): continue self.process(data, child, history[:])
python
def process(self, data, type, history): """ process the specified type then process its children """ if type in history: return if type.enum(): return history.append(type) resolved = type.resolve() value = None if type.multi_occurrence(): value = [] else: if len(resolved) > 0: if resolved.mixed(): value = Factory.property(resolved.name) md = value.__metadata__ md.sxtype = resolved else: value = Factory.object(resolved.name) md = value.__metadata__ md.sxtype = resolved md.ordering = self.ordering(resolved) setattr(data, type.name, value) if value is not None: data = value if not isinstance(data, list): self.add_attributes(data, resolved) for child, ancestry in resolved.children(): if self.skip_child(child, ancestry): continue self.process(data, child, history[:])
[ "def", "process", "(", "self", ",", "data", ",", "type", ",", "history", ")", ":", "if", "type", "in", "history", ":", "return", "if", "type", ".", "enum", "(", ")", ":", "return", "history", ".", "append", "(", "type", ")", "resolved", "=", "type", ".", "resolve", "(", ")", "value", "=", "None", "if", "type", ".", "multi_occurrence", "(", ")", ":", "value", "=", "[", "]", "else", ":", "if", "len", "(", "resolved", ")", ">", "0", ":", "if", "resolved", ".", "mixed", "(", ")", ":", "value", "=", "Factory", ".", "property", "(", "resolved", ".", "name", ")", "md", "=", "value", ".", "__metadata__", "md", ".", "sxtype", "=", "resolved", "else", ":", "value", "=", "Factory", ".", "object", "(", "resolved", ".", "name", ")", "md", "=", "value", ".", "__metadata__", "md", ".", "sxtype", "=", "resolved", "md", ".", "ordering", "=", "self", ".", "ordering", "(", "resolved", ")", "setattr", "(", "data", ",", "type", ".", "name", ",", "value", ")", "if", "value", "is", "not", "None", ":", "data", "=", "value", "if", "not", "isinstance", "(", "data", ",", "list", ")", ":", "self", ".", "add_attributes", "(", "data", ",", "resolved", ")", "for", "child", ",", "ancestry", "in", "resolved", ".", "children", "(", ")", ":", "if", "self", ".", "skip_child", "(", "child", ",", "ancestry", ")", ":", "continue", "self", ".", "process", "(", "data", ",", "child", ",", "history", "[", ":", "]", ")" ]
process the specified type then process its children
[ "process", "the", "specified", "type", "then", "process", "its", "children" ]
e5b540792206a41efc22f5d5b9cfac2dbe7a7992
https://github.com/ovnicraft/suds2/blob/e5b540792206a41efc22f5d5b9cfac2dbe7a7992/suds/builder.py#L60-L90
train
ovnicraft/suds2
suds/builder.py
Builder.skip_child
def skip_child(self, child, ancestry): """ get whether or not to skip the specified child """ if child.any(): return True for x in ancestry: if x.choice(): return True return False
python
def skip_child(self, child, ancestry): """ get whether or not to skip the specified child """ if child.any(): return True for x in ancestry: if x.choice(): return True return False
[ "def", "skip_child", "(", "self", ",", "child", ",", "ancestry", ")", ":", "if", "child", ".", "any", "(", ")", ":", "return", "True", "for", "x", "in", "ancestry", ":", "if", "x", ".", "choice", "(", ")", ":", "return", "True", "return", "False" ]
get whether or not to skip the specified child
[ "get", "whether", "or", "not", "to", "skip", "the", "specified", "child" ]
e5b540792206a41efc22f5d5b9cfac2dbe7a7992
https://github.com/ovnicraft/suds2/blob/e5b540792206a41efc22f5d5b9cfac2dbe7a7992/suds/builder.py#L99-L105
train
nephila/django-knocker
knocker/signals.py
active_knocks
def active_knocks(obj): """ Checks whether knocks are enabled for the model given as argument :param obj: model instance :return True if knocks are active """ if not hasattr(_thread_locals, 'knock_enabled'): return True return _thread_locals.knock_enabled.get(obj.__class__, True)
python
def active_knocks(obj): """ Checks whether knocks are enabled for the model given as argument :param obj: model instance :return True if knocks are active """ if not hasattr(_thread_locals, 'knock_enabled'): return True return _thread_locals.knock_enabled.get(obj.__class__, True)
[ "def", "active_knocks", "(", "obj", ")", ":", "if", "not", "hasattr", "(", "_thread_locals", ",", "'knock_enabled'", ")", ":", "return", "True", "return", "_thread_locals", ".", "knock_enabled", ".", "get", "(", "obj", ".", "__class__", ",", "True", ")" ]
Checks whether knocks are enabled for the model given as argument :param obj: model instance :return True if knocks are active
[ "Checks", "whether", "knocks", "are", "enabled", "for", "the", "model", "given", "as", "argument" ]
d25380d43a1f91285f1581dcf9db8510fe87f354
https://github.com/nephila/django-knocker/blob/d25380d43a1f91285f1581dcf9db8510fe87f354/knocker/signals.py#L34-L43
train
nephila/django-knocker
knocker/signals.py
pause_knocks
def pause_knocks(obj): """ Context manager to suspend sending knocks for the given model :param obj: model instance """ if not hasattr(_thread_locals, 'knock_enabled'): _thread_locals.knock_enabled = {} obj.__class__._disconnect() _thread_locals.knock_enabled[obj.__class__] = False yield _thread_locals.knock_enabled[obj.__class__] = True obj.__class__._connect()
python
def pause_knocks(obj): """ Context manager to suspend sending knocks for the given model :param obj: model instance """ if not hasattr(_thread_locals, 'knock_enabled'): _thread_locals.knock_enabled = {} obj.__class__._disconnect() _thread_locals.knock_enabled[obj.__class__] = False yield _thread_locals.knock_enabled[obj.__class__] = True obj.__class__._connect()
[ "def", "pause_knocks", "(", "obj", ")", ":", "if", "not", "hasattr", "(", "_thread_locals", ",", "'knock_enabled'", ")", ":", "_thread_locals", ".", "knock_enabled", "=", "{", "}", "obj", ".", "__class__", ".", "_disconnect", "(", ")", "_thread_locals", ".", "knock_enabled", "[", "obj", ".", "__class__", "]", "=", "False", "yield", "_thread_locals", ".", "knock_enabled", "[", "obj", ".", "__class__", "]", "=", "True", "obj", ".", "__class__", ".", "_connect", "(", ")" ]
Context manager to suspend sending knocks for the given model :param obj: model instance
[ "Context", "manager", "to", "suspend", "sending", "knocks", "for", "the", "given", "model" ]
d25380d43a1f91285f1581dcf9db8510fe87f354
https://github.com/nephila/django-knocker/blob/d25380d43a1f91285f1581dcf9db8510fe87f354/knocker/signals.py#L47-L59
train
tonybaloney/retox
retox/reporter.py
RetoxReporter._loopreport
def _loopreport(self): ''' Loop over the report progress ''' while 1: eventlet.sleep(0.2) ac2popenlist = {} for action in self.session._actions: for popen in action._popenlist: if popen.poll() is None: lst = ac2popenlist.setdefault(action.activity, []) lst.append(popen) if not action._popenlist and action in self._actionmayfinish: super(RetoxReporter, self).logaction_finish(action) self._actionmayfinish.remove(action) self.screen.draw_next_frame(repeat=False)
python
def _loopreport(self): ''' Loop over the report progress ''' while 1: eventlet.sleep(0.2) ac2popenlist = {} for action in self.session._actions: for popen in action._popenlist: if popen.poll() is None: lst = ac2popenlist.setdefault(action.activity, []) lst.append(popen) if not action._popenlist and action in self._actionmayfinish: super(RetoxReporter, self).logaction_finish(action) self._actionmayfinish.remove(action) self.screen.draw_next_frame(repeat=False)
[ "def", "_loopreport", "(", "self", ")", ":", "while", "1", ":", "eventlet", ".", "sleep", "(", "0.2", ")", "ac2popenlist", "=", "{", "}", "for", "action", "in", "self", ".", "session", ".", "_actions", ":", "for", "popen", "in", "action", ".", "_popenlist", ":", "if", "popen", ".", "poll", "(", ")", "is", "None", ":", "lst", "=", "ac2popenlist", ".", "setdefault", "(", "action", ".", "activity", ",", "[", "]", ")", "lst", ".", "append", "(", "popen", ")", "if", "not", "action", ".", "_popenlist", "and", "action", "in", "self", ".", "_actionmayfinish", ":", "super", "(", "RetoxReporter", ",", "self", ")", ".", "logaction_finish", "(", "action", ")", "self", ".", "_actionmayfinish", ".", "remove", "(", "action", ")", "self", ".", "screen", ".", "draw_next_frame", "(", "repeat", "=", "False", ")" ]
Loop over the report progress
[ "Loop", "over", "the", "report", "progress" ]
4635e31001d2ac083423f46766249ac8daca7c9c
https://github.com/tonybaloney/retox/blob/4635e31001d2ac083423f46766249ac8daca7c9c/retox/reporter.py#L49-L65
train
yejianye/mdmail
mdmail/api.py
send
def send(email, subject=None, from_email=None, to_email=None, cc=None, bcc=None, reply_to=None, smtp=None): """Send markdown email Args: email (str/obj): A markdown string or EmailContent object subject (str): subject line from_email (str): sender email address to_email (str/list): recipient email addresses cc (str/list): CC email addresses (string or a list) bcc (str/list): BCC email addresses (string or a list) reply_to (str): Reply-to email address smtp (dict): SMTP configuration (dict) Schema of smtp dict: host (str): SMTP server host. Default: localhost port (int): SMTP server port. Default: 25 tls (bool): Use TLS. Default: False ssl (bool): Use SSL. Default: False user (bool): SMTP login user. Default empty password (bool): SMTP login password. Default empty """ if is_string(email): email = EmailContent(email) from_email = sanitize_email_address(from_email or email.headers.get('from')) to_email = sanitize_email_address(to_email or email.headers.get('to')) cc = sanitize_email_address(cc or email.headers.get('cc')) bcc = sanitize_email_address(bcc or email.headers.get('bcc')) reply_to = sanitize_email_address(reply_to or email.headers.get('reply-to')) message_args = { 'html': email.html, 'text': email.text, 'subject': (subject or email.headers.get('subject', '')), 'mail_from': from_email, 'mail_to': to_email } if cc: message_args['cc'] = cc if bcc: message_args['bcc'] = bcc if reply_to: message_args['headers'] = {'reply-to': reply_to} message = emails.Message(**message_args) for filename, data in email.inline_images: message.attach(filename=filename, content_disposition='inline', data=data) message.send(smtp=smtp)
python
def send(email, subject=None, from_email=None, to_email=None, cc=None, bcc=None, reply_to=None, smtp=None): """Send markdown email Args: email (str/obj): A markdown string or EmailContent object subject (str): subject line from_email (str): sender email address to_email (str/list): recipient email addresses cc (str/list): CC email addresses (string or a list) bcc (str/list): BCC email addresses (string or a list) reply_to (str): Reply-to email address smtp (dict): SMTP configuration (dict) Schema of smtp dict: host (str): SMTP server host. Default: localhost port (int): SMTP server port. Default: 25 tls (bool): Use TLS. Default: False ssl (bool): Use SSL. Default: False user (bool): SMTP login user. Default empty password (bool): SMTP login password. Default empty """ if is_string(email): email = EmailContent(email) from_email = sanitize_email_address(from_email or email.headers.get('from')) to_email = sanitize_email_address(to_email or email.headers.get('to')) cc = sanitize_email_address(cc or email.headers.get('cc')) bcc = sanitize_email_address(bcc or email.headers.get('bcc')) reply_to = sanitize_email_address(reply_to or email.headers.get('reply-to')) message_args = { 'html': email.html, 'text': email.text, 'subject': (subject or email.headers.get('subject', '')), 'mail_from': from_email, 'mail_to': to_email } if cc: message_args['cc'] = cc if bcc: message_args['bcc'] = bcc if reply_to: message_args['headers'] = {'reply-to': reply_to} message = emails.Message(**message_args) for filename, data in email.inline_images: message.attach(filename=filename, content_disposition='inline', data=data) message.send(smtp=smtp)
[ "def", "send", "(", "email", ",", "subject", "=", "None", ",", "from_email", "=", "None", ",", "to_email", "=", "None", ",", "cc", "=", "None", ",", "bcc", "=", "None", ",", "reply_to", "=", "None", ",", "smtp", "=", "None", ")", ":", "if", "is_string", "(", "email", ")", ":", "email", "=", "EmailContent", "(", "email", ")", "from_email", "=", "sanitize_email_address", "(", "from_email", "or", "email", ".", "headers", ".", "get", "(", "'from'", ")", ")", "to_email", "=", "sanitize_email_address", "(", "to_email", "or", "email", ".", "headers", ".", "get", "(", "'to'", ")", ")", "cc", "=", "sanitize_email_address", "(", "cc", "or", "email", ".", "headers", ".", "get", "(", "'cc'", ")", ")", "bcc", "=", "sanitize_email_address", "(", "bcc", "or", "email", ".", "headers", ".", "get", "(", "'bcc'", ")", ")", "reply_to", "=", "sanitize_email_address", "(", "reply_to", "or", "email", ".", "headers", ".", "get", "(", "'reply-to'", ")", ")", "message_args", "=", "{", "'html'", ":", "email", ".", "html", ",", "'text'", ":", "email", ".", "text", ",", "'subject'", ":", "(", "subject", "or", "email", ".", "headers", ".", "get", "(", "'subject'", ",", "''", ")", ")", ",", "'mail_from'", ":", "from_email", ",", "'mail_to'", ":", "to_email", "}", "if", "cc", ":", "message_args", "[", "'cc'", "]", "=", "cc", "if", "bcc", ":", "message_args", "[", "'bcc'", "]", "=", "bcc", "if", "reply_to", ":", "message_args", "[", "'headers'", "]", "=", "{", "'reply-to'", ":", "reply_to", "}", "message", "=", "emails", ".", "Message", "(", "*", "*", "message_args", ")", "for", "filename", ",", "data", "in", "email", ".", "inline_images", ":", "message", ".", "attach", "(", "filename", "=", "filename", ",", "content_disposition", "=", "'inline'", ",", "data", "=", "data", ")", "message", ".", "send", "(", "smtp", "=", "smtp", ")" ]
Send markdown email Args: email (str/obj): A markdown string or EmailContent object subject (str): subject line from_email (str): sender email address to_email (str/list): recipient email addresses cc (str/list): CC email addresses (string or a list) bcc (str/list): BCC email addresses (string or a list) reply_to (str): Reply-to email address smtp (dict): SMTP configuration (dict) Schema of smtp dict: host (str): SMTP server host. Default: localhost port (int): SMTP server port. Default: 25 tls (bool): Use TLS. Default: False ssl (bool): Use SSL. Default: False user (bool): SMTP login user. Default empty password (bool): SMTP login password. Default empty
[ "Send", "markdown", "email" ]
ef03da8d5836b5ae0a4ad8c44f2fe4936a896644
https://github.com/yejianye/mdmail/blob/ef03da8d5836b5ae0a4ad8c44f2fe4936a896644/mdmail/api.py#L11-L63
train
marrow/mongo
marrow/mongo/core/field/date.py
Date._process_tz
def _process_tz(self, dt, naive, tz): """Process timezone casting and conversion.""" def _tz(t): if t in (None, 'naive'): return t if t == 'local': if __debug__ and not localtz: raise ValueError("Requested conversion to local timezone, but `localtz` not installed.") t = localtz if not isinstance(t, tzinfo): if __debug__ and not localtz: raise ValueError("The `pytz` package must be installed to look up timezone: " + repr(t)) t = get_tz(t) if not hasattr(t, 'normalize') and get_tz: # Attempt to handle non-pytz tzinfo. t = get_tz(t.tzname(dt)) return t naive = _tz(naive) tz = _tz(tz) if not dt.tzinfo and naive: if hasattr(naive, 'localize'): dt = naive.localize(dt) else: dt = dt.replace(tzinfo=naive) if not tz: return dt if hasattr(tz, 'normalize'): dt = tz.normalize(dt.astimezone(tz)) elif tz == 'naive': dt = dt.replace(tzinfo=None) else: dt = dt.astimezone(tz) # Warning: this might not always be entirely correct! return dt
python
def _process_tz(self, dt, naive, tz): """Process timezone casting and conversion.""" def _tz(t): if t in (None, 'naive'): return t if t == 'local': if __debug__ and not localtz: raise ValueError("Requested conversion to local timezone, but `localtz` not installed.") t = localtz if not isinstance(t, tzinfo): if __debug__ and not localtz: raise ValueError("The `pytz` package must be installed to look up timezone: " + repr(t)) t = get_tz(t) if not hasattr(t, 'normalize') and get_tz: # Attempt to handle non-pytz tzinfo. t = get_tz(t.tzname(dt)) return t naive = _tz(naive) tz = _tz(tz) if not dt.tzinfo and naive: if hasattr(naive, 'localize'): dt = naive.localize(dt) else: dt = dt.replace(tzinfo=naive) if not tz: return dt if hasattr(tz, 'normalize'): dt = tz.normalize(dt.astimezone(tz)) elif tz == 'naive': dt = dt.replace(tzinfo=None) else: dt = dt.astimezone(tz) # Warning: this might not always be entirely correct! return dt
[ "def", "_process_tz", "(", "self", ",", "dt", ",", "naive", ",", "tz", ")", ":", "def", "_tz", "(", "t", ")", ":", "if", "t", "in", "(", "None", ",", "'naive'", ")", ":", "return", "t", "if", "t", "==", "'local'", ":", "if", "__debug__", "and", "not", "localtz", ":", "raise", "ValueError", "(", "\"Requested conversion to local timezone, but `localtz` not installed.\"", ")", "t", "=", "localtz", "if", "not", "isinstance", "(", "t", ",", "tzinfo", ")", ":", "if", "__debug__", "and", "not", "localtz", ":", "raise", "ValueError", "(", "\"The `pytz` package must be installed to look up timezone: \"", "+", "repr", "(", "t", ")", ")", "t", "=", "get_tz", "(", "t", ")", "if", "not", "hasattr", "(", "t", ",", "'normalize'", ")", "and", "get_tz", ":", "# Attempt to handle non-pytz tzinfo.", "t", "=", "get_tz", "(", "t", ".", "tzname", "(", "dt", ")", ")", "return", "t", "naive", "=", "_tz", "(", "naive", ")", "tz", "=", "_tz", "(", "tz", ")", "if", "not", "dt", ".", "tzinfo", "and", "naive", ":", "if", "hasattr", "(", "naive", ",", "'localize'", ")", ":", "dt", "=", "naive", ".", "localize", "(", "dt", ")", "else", ":", "dt", "=", "dt", ".", "replace", "(", "tzinfo", "=", "naive", ")", "if", "not", "tz", ":", "return", "dt", "if", "hasattr", "(", "tz", ",", "'normalize'", ")", ":", "dt", "=", "tz", ".", "normalize", "(", "dt", ".", "astimezone", "(", "tz", ")", ")", "elif", "tz", "==", "'naive'", ":", "dt", "=", "dt", ".", "replace", "(", "tzinfo", "=", "None", ")", "else", ":", "dt", "=", "dt", ".", "astimezone", "(", "tz", ")", "# Warning: this might not always be entirely correct!", "return", "dt" ]
Process timezone casting and conversion.
[ "Process", "timezone", "casting", "and", "conversion", "." ]
2066dc73e281b8a46cb5fc965267d6b8e1b18467
https://github.com/marrow/mongo/blob/2066dc73e281b8a46cb5fc965267d6b8e1b18467/marrow/mongo/core/field/date.py#L59-L102
train
marrow/mongo
marrow/mongo/core/document.py
Document._prepare_defaults
def _prepare_defaults(self): """Trigger assignment of default values.""" for name, field in self.__fields__.items(): if field.assign: getattr(self, name)
python
def _prepare_defaults(self): """Trigger assignment of default values.""" for name, field in self.__fields__.items(): if field.assign: getattr(self, name)
[ "def", "_prepare_defaults", "(", "self", ")", ":", "for", "name", ",", "field", "in", "self", ".", "__fields__", ".", "items", "(", ")", ":", "if", "field", ".", "assign", ":", "getattr", "(", "self", ",", "name", ")" ]
Trigger assignment of default values.
[ "Trigger", "assignment", "of", "default", "values", "." ]
2066dc73e281b8a46cb5fc965267d6b8e1b18467
https://github.com/marrow/mongo/blob/2066dc73e281b8a46cb5fc965267d6b8e1b18467/marrow/mongo/core/document.py#L71-L76
train
marrow/mongo
marrow/mongo/core/document.py
Document.from_mongo
def from_mongo(cls, doc): """Convert data coming in from the MongoDB wire driver into a Document instance.""" if doc is None: # To support simplified iterative use, None should return None. return None if isinstance(doc, Document): # No need to perform processing on existing Document instances. return doc if cls.__type_store__ and cls.__type_store__ in doc: # Instantiate specific class mentioned in the data. cls = load(doc[cls.__type_store__], 'marrow.mongo.document') # Prepare a new instance in such a way that changes to the instance will be reflected in the originating doc. instance = cls(_prepare_defaults=False) # Construct an instance, but delay default value processing. instance.__data__ = doc # I am Popeye of Borg (pattern); you will be askimilgrated. instance._prepare_defaults() # pylint:disable=protected-access -- deferred default value processing. return instance
python
def from_mongo(cls, doc): """Convert data coming in from the MongoDB wire driver into a Document instance.""" if doc is None: # To support simplified iterative use, None should return None. return None if isinstance(doc, Document): # No need to perform processing on existing Document instances. return doc if cls.__type_store__ and cls.__type_store__ in doc: # Instantiate specific class mentioned in the data. cls = load(doc[cls.__type_store__], 'marrow.mongo.document') # Prepare a new instance in such a way that changes to the instance will be reflected in the originating doc. instance = cls(_prepare_defaults=False) # Construct an instance, but delay default value processing. instance.__data__ = doc # I am Popeye of Borg (pattern); you will be askimilgrated. instance._prepare_defaults() # pylint:disable=protected-access -- deferred default value processing. return instance
[ "def", "from_mongo", "(", "cls", ",", "doc", ")", ":", "if", "doc", "is", "None", ":", "# To support simplified iterative use, None should return None.", "return", "None", "if", "isinstance", "(", "doc", ",", "Document", ")", ":", "# No need to perform processing on existing Document instances.", "return", "doc", "if", "cls", ".", "__type_store__", "and", "cls", ".", "__type_store__", "in", "doc", ":", "# Instantiate specific class mentioned in the data.", "cls", "=", "load", "(", "doc", "[", "cls", ".", "__type_store__", "]", ",", "'marrow.mongo.document'", ")", "# Prepare a new instance in such a way that changes to the instance will be reflected in the originating doc.", "instance", "=", "cls", "(", "_prepare_defaults", "=", "False", ")", "# Construct an instance, but delay default value processing.", "instance", ".", "__data__", "=", "doc", "# I am Popeye of Borg (pattern); you will be askimilgrated.", "instance", ".", "_prepare_defaults", "(", ")", "# pylint:disable=protected-access -- deferred default value processing.", "return", "instance" ]
Convert data coming in from the MongoDB wire driver into a Document instance.
[ "Convert", "data", "coming", "in", "from", "the", "MongoDB", "wire", "driver", "into", "a", "Document", "instance", "." ]
2066dc73e281b8a46cb5fc965267d6b8e1b18467
https://github.com/marrow/mongo/blob/2066dc73e281b8a46cb5fc965267d6b8e1b18467/marrow/mongo/core/document.py#L81-L98
train
marrow/mongo
marrow/mongo/core/document.py
Document.pop
def pop(self, name, default=SENTINEL): """Retrieve and remove a value from the backing store, optionally with a default.""" if default is SENTINEL: return self.__data__.pop(name) return self.__data__.pop(name, default)
python
def pop(self, name, default=SENTINEL): """Retrieve and remove a value from the backing store, optionally with a default.""" if default is SENTINEL: return self.__data__.pop(name) return self.__data__.pop(name, default)
[ "def", "pop", "(", "self", ",", "name", ",", "default", "=", "SENTINEL", ")", ":", "if", "default", "is", "SENTINEL", ":", "return", "self", ".", "__data__", ".", "pop", "(", "name", ")", "return", "self", ".", "__data__", ".", "pop", "(", "name", ",", "default", ")" ]
Retrieve and remove a value from the backing store, optionally with a default.
[ "Retrieve", "and", "remove", "a", "value", "from", "the", "backing", "store", "optionally", "with", "a", "default", "." ]
2066dc73e281b8a46cb5fc965267d6b8e1b18467
https://github.com/marrow/mongo/blob/2066dc73e281b8a46cb5fc965267d6b8e1b18467/marrow/mongo/core/document.py#L246-L252
train
marrow/mongo
marrow/mongo/query/query.py
Q._op
def _op(self, operation, other, *allowed): """A basic operation operating on a single value.""" f = self._field if self._combining: # We are a field-compound query fragment, e.g. (Foo.bar & Foo.baz). return reduce(self._combining, (q._op(operation, other, *allowed) for q in f)) # pylint:disable=protected-access # Optimize this away in production; diagnosic aide. if __debug__ and _complex_safety_check(f, {operation} | set(allowed)): # pragma: no cover raise NotImplementedError("{self!r} does not allow {op} comparison.".format(self=self, op=operation)) if other is not None: other = f.transformer.foreign(other, (f, self._document)) return Filter({self._name: {operation: other}})
python
def _op(self, operation, other, *allowed): """A basic operation operating on a single value.""" f = self._field if self._combining: # We are a field-compound query fragment, e.g. (Foo.bar & Foo.baz). return reduce(self._combining, (q._op(operation, other, *allowed) for q in f)) # pylint:disable=protected-access # Optimize this away in production; diagnosic aide. if __debug__ and _complex_safety_check(f, {operation} | set(allowed)): # pragma: no cover raise NotImplementedError("{self!r} does not allow {op} comparison.".format(self=self, op=operation)) if other is not None: other = f.transformer.foreign(other, (f, self._document)) return Filter({self._name: {operation: other}})
[ "def", "_op", "(", "self", ",", "operation", ",", "other", ",", "*", "allowed", ")", ":", "f", "=", "self", ".", "_field", "if", "self", ".", "_combining", ":", "# We are a field-compound query fragment, e.g. (Foo.bar & Foo.baz).", "return", "reduce", "(", "self", ".", "_combining", ",", "(", "q", ".", "_op", "(", "operation", ",", "other", ",", "*", "allowed", ")", "for", "q", "in", "f", ")", ")", "# pylint:disable=protected-access", "# Optimize this away in production; diagnosic aide.", "if", "__debug__", "and", "_complex_safety_check", "(", "f", ",", "{", "operation", "}", "|", "set", "(", "allowed", ")", ")", ":", "# pragma: no cover", "raise", "NotImplementedError", "(", "\"{self!r} does not allow {op} comparison.\"", ".", "format", "(", "self", "=", "self", ",", "op", "=", "operation", ")", ")", "if", "other", "is", "not", "None", ":", "other", "=", "f", ".", "transformer", ".", "foreign", "(", "other", ",", "(", "f", ",", "self", ".", "_document", ")", ")", "return", "Filter", "(", "{", "self", ".", "_name", ":", "{", "operation", ":", "other", "}", "}", ")" ]
A basic operation operating on a single value.
[ "A", "basic", "operation", "operating", "on", "a", "single", "value", "." ]
2066dc73e281b8a46cb5fc965267d6b8e1b18467
https://github.com/marrow/mongo/blob/2066dc73e281b8a46cb5fc965267d6b8e1b18467/marrow/mongo/query/query.py#L154-L170
train
marrow/mongo
marrow/mongo/query/query.py
Q._iop
def _iop(self, operation, other, *allowed): """An iterative operation operating on multiple values. Consumes iterators to construct a concrete list at time of execution. """ f = self._field if self._combining: # We are a field-compound query fragment, e.g. (Foo.bar & Foo.baz). return reduce(self._combining, (q._iop(operation, other, *allowed) for q in f)) # pylint:disable=protected-access # Optimize this away in production; diagnosic aide. if __debug__ and _complex_safety_check(f, {operation} | set(allowed)): # pragma: no cover raise NotImplementedError("{self!r} does not allow {op} comparison.".format( self=self, op=operation)) def _t(o): for value in o: yield None if value is None else f.transformer.foreign(value, (f, self._document)) other = other if len(other) > 1 else other[0] values = list(_t(other)) return Filter({self._name: {operation: values}})
python
def _iop(self, operation, other, *allowed): """An iterative operation operating on multiple values. Consumes iterators to construct a concrete list at time of execution. """ f = self._field if self._combining: # We are a field-compound query fragment, e.g. (Foo.bar & Foo.baz). return reduce(self._combining, (q._iop(operation, other, *allowed) for q in f)) # pylint:disable=protected-access # Optimize this away in production; diagnosic aide. if __debug__ and _complex_safety_check(f, {operation} | set(allowed)): # pragma: no cover raise NotImplementedError("{self!r} does not allow {op} comparison.".format( self=self, op=operation)) def _t(o): for value in o: yield None if value is None else f.transformer.foreign(value, (f, self._document)) other = other if len(other) > 1 else other[0] values = list(_t(other)) return Filter({self._name: {operation: values}})
[ "def", "_iop", "(", "self", ",", "operation", ",", "other", ",", "*", "allowed", ")", ":", "f", "=", "self", ".", "_field", "if", "self", ".", "_combining", ":", "# We are a field-compound query fragment, e.g. (Foo.bar & Foo.baz).", "return", "reduce", "(", "self", ".", "_combining", ",", "(", "q", ".", "_iop", "(", "operation", ",", "other", ",", "*", "allowed", ")", "for", "q", "in", "f", ")", ")", "# pylint:disable=protected-access", "# Optimize this away in production; diagnosic aide.", "if", "__debug__", "and", "_complex_safety_check", "(", "f", ",", "{", "operation", "}", "|", "set", "(", "allowed", ")", ")", ":", "# pragma: no cover", "raise", "NotImplementedError", "(", "\"{self!r} does not allow {op} comparison.\"", ".", "format", "(", "self", "=", "self", ",", "op", "=", "operation", ")", ")", "def", "_t", "(", "o", ")", ":", "for", "value", "in", "o", ":", "yield", "None", "if", "value", "is", "None", "else", "f", ".", "transformer", ".", "foreign", "(", "value", ",", "(", "f", ",", "self", ".", "_document", ")", ")", "other", "=", "other", "if", "len", "(", "other", ")", ">", "1", "else", "other", "[", "0", "]", "values", "=", "list", "(", "_t", "(", "other", ")", ")", "return", "Filter", "(", "{", "self", ".", "_name", ":", "{", "operation", ":", "values", "}", "}", ")" ]
An iterative operation operating on multiple values. Consumes iterators to construct a concrete list at time of execution.
[ "An", "iterative", "operation", "operating", "on", "multiple", "values", ".", "Consumes", "iterators", "to", "construct", "a", "concrete", "list", "at", "time", "of", "execution", "." ]
2066dc73e281b8a46cb5fc965267d6b8e1b18467
https://github.com/marrow/mongo/blob/2066dc73e281b8a46cb5fc965267d6b8e1b18467/marrow/mongo/query/query.py#L172-L196
train