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Semeru Lab 7

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

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]]

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)

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.

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)

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.

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)

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]

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)

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.

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))

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.

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)

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.

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 != []]

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

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

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)

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()

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

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)

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

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)

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

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

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

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 {}

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

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

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)

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()

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))

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")

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', )

Define basic command-line arguments required by the script. @parser is a parser object created using the `argparse` module. returns: None

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

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

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)

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

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

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))

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)

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)

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)

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)

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 {} )

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()

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

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?

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

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

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

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

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

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

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);

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]]

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

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

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

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)

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)

Removes empty line. Example usage:: {% emptylineless %} test1 test2 test3 {% endemptylineless %} This example would return this HTML:: test1 test2 test3

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

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

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))

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))

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)

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()

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)

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')

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 });')

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)

Get a character set with individual members or ranges. Current index is on '[', the start of the character set.

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)

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)

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)

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

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

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)

Establish the connection. This is done automatically for you. If you lose the connection, you can manually run this to be re-connected.

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)

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()

Create a folder on S3. Examples -------- >>> s3utils.mkdir("path/to/my_folder") Making directory: path/to/my_folder

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)

Delete the path and anything under the path. Example ------- >>> s3utils.rm("path/to/file_or_folder")

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

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

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'}

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)

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

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, )

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.

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()

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")

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)

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" } ], }

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

Get the path from a given url, including the querystring. Args: url (str) Returns: str

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)

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

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)

Firms search in rubric http://api.2gis.ru/doc/firms/searches/searchinrubric/

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)

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()

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`

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()

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`

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()

Move laggard tasks over :param activity: The virtualenv status :type activity: ``str``

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()

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)}

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()

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)

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[:])

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

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)

Checks whether knocks are enabled for the model given as argument :param obj: model instance :return True if knocks are active

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()

Context manager to suspend sending knocks for the given model :param obj: model instance

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)

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)

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

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

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)

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

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)

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}})

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}})

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