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2,200 | esheldon/fitsio | fitsio/header.py | FITSHDR.next | def next(self):
"""
for iteration over the header entries
"""
if self._current < len(self._record_list):
rec = self._record_list[self._current]
key = rec['name']
self._current += 1
return key
else:
raise StopIteration | python | def next(self):
"""
for iteration over the header entries
"""
if self._current < len(self._record_list):
rec = self._record_list[self._current]
key = rec['name']
self._current += 1
return key
else:
raise StopIteration | [
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2,201 | esheldon/fitsio | fitsio/header.py | FITSRecord.set_record | def set_record(self, record, **kw):
"""
check the record is valid and set keys in the dict
parameters
----------
record: string
Dict representing a record or a string representing a FITS header
card
"""
if isstring(record):
card = FITSCard(record)
self.update(card)
self.verify()
else:
if isinstance(record, FITSRecord):
self.update(record)
elif isinstance(record, dict):
if 'name' in record and 'value' in record:
self.update(record)
elif 'card_string' in record:
self.set_record(record['card_string'])
else:
raise ValueError('record must have name,value fields '
'or a card_string field')
else:
raise ValueError("record must be a string card or "
"dictionary or FITSRecord") | python | def set_record(self, record, **kw):
"""
check the record is valid and set keys in the dict
parameters
----------
record: string
Dict representing a record or a string representing a FITS header
card
"""
if isstring(record):
card = FITSCard(record)
self.update(card)
self.verify()
else:
if isinstance(record, FITSRecord):
self.update(record)
elif isinstance(record, dict):
if 'name' in record and 'value' in record:
self.update(record)
elif 'card_string' in record:
self.set_record(record['card_string'])
else:
raise ValueError('record must have name,value fields '
'or a card_string field')
else:
raise ValueError("record must be a string card or "
"dictionary or FITSRecord") | [
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2,202 | esheldon/fitsio | fitsio/header.py | FITSCard._check_equals | def _check_equals(self):
"""
check for = in position 8, set attribute _has_equals
"""
card_string = self['card_string']
if len(card_string) < 9:
self._has_equals = False
elif card_string[8] == '=':
self._has_equals = True
else:
self._has_equals = False | python | def _check_equals(self):
"""
check for = in position 8, set attribute _has_equals
"""
card_string = self['card_string']
if len(card_string) < 9:
self._has_equals = False
elif card_string[8] == '=':
self._has_equals = True
else:
self._has_equals = False | [
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2,203 | esheldon/fitsio | fitsio/header.py | FITSCard._convert_value | def _convert_value(self, value_orig):
"""
things like 6 and 1.25 are converted with ast.literal_value
Things like 'hello' are stripped of quotes
"""
import ast
if value_orig is None:
return value_orig
if value_orig.startswith("'") and value_orig.endswith("'"):
value = value_orig[1:-1]
else:
try:
avalue = ast.parse(value_orig).body[0].value
if isinstance(avalue, ast.BinOp):
# this is probably a string that happens to look like
# a binary operation, e.g. '25-3'
value = value_orig
else:
value = ast.literal_eval(value_orig)
except Exception:
value = self._convert_string(value_orig)
if isinstance(value, int) and '_' in value_orig:
value = value_orig
return value | python | def _convert_value(self, value_orig):
"""
things like 6 and 1.25 are converted with ast.literal_value
Things like 'hello' are stripped of quotes
"""
import ast
if value_orig is None:
return value_orig
if value_orig.startswith("'") and value_orig.endswith("'"):
value = value_orig[1:-1]
else:
try:
avalue = ast.parse(value_orig).body[0].value
if isinstance(avalue, ast.BinOp):
# this is probably a string that happens to look like
# a binary operation, e.g. '25-3'
value = value_orig
else:
value = ast.literal_eval(value_orig)
except Exception:
value = self._convert_string(value_orig)
if isinstance(value, int) and '_' in value_orig:
value = value_orig
return value | [
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2,204 | sanger-pathogens/ariba | ariba/cluster.py | Cluster._make_reads_for_assembly | def _make_reads_for_assembly(number_of_wanted_reads, total_reads, reads_in1, reads_in2, reads_out1, reads_out2, random_seed=None):
'''Makes fastq files that are random subset of input files. Returns total number of reads in output files.
If the number of wanted reads is >= total reads, then just makes symlinks instead of making
new copies of the input files.'''
random.seed(random_seed)
if number_of_wanted_reads < total_reads:
reads_written = 0
percent_wanted = 100 * number_of_wanted_reads / total_reads
file_reader1 = pyfastaq.sequences.file_reader(reads_in1)
file_reader2 = pyfastaq.sequences.file_reader(reads_in2)
out1 = pyfastaq.utils.open_file_write(reads_out1)
out2 = pyfastaq.utils.open_file_write(reads_out2)
for read1 in file_reader1:
try:
read2 = next(file_reader2)
except StopIteration:
pyfastaq.utils.close(out1)
pyfastaq.utils.close(out2)
raise Error('Error subsetting reads. No mate found for read ' + read1.id)
if random.randint(0, 100) <= percent_wanted:
print(read1, file=out1)
print(read2, file=out2)
reads_written += 2
pyfastaq.utils.close(out1)
pyfastaq.utils.close(out2)
return reads_written
else:
os.symlink(reads_in1, reads_out1)
os.symlink(reads_in2, reads_out2)
return total_reads | python | def _make_reads_for_assembly(number_of_wanted_reads, total_reads, reads_in1, reads_in2, reads_out1, reads_out2, random_seed=None):
'''Makes fastq files that are random subset of input files. Returns total number of reads in output files.
If the number of wanted reads is >= total reads, then just makes symlinks instead of making
new copies of the input files.'''
random.seed(random_seed)
if number_of_wanted_reads < total_reads:
reads_written = 0
percent_wanted = 100 * number_of_wanted_reads / total_reads
file_reader1 = pyfastaq.sequences.file_reader(reads_in1)
file_reader2 = pyfastaq.sequences.file_reader(reads_in2)
out1 = pyfastaq.utils.open_file_write(reads_out1)
out2 = pyfastaq.utils.open_file_write(reads_out2)
for read1 in file_reader1:
try:
read2 = next(file_reader2)
except StopIteration:
pyfastaq.utils.close(out1)
pyfastaq.utils.close(out2)
raise Error('Error subsetting reads. No mate found for read ' + read1.id)
if random.randint(0, 100) <= percent_wanted:
print(read1, file=out1)
print(read2, file=out2)
reads_written += 2
pyfastaq.utils.close(out1)
pyfastaq.utils.close(out2)
return reads_written
else:
os.symlink(reads_in1, reads_out1)
os.symlink(reads_in2, reads_out2)
return total_reads | [
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2,205 | sanger-pathogens/ariba | ariba/tb.py | load_mutations | def load_mutations(gene_coords, mutation_to_drug_json, variants_txt, upstream_before=100):
'''Load mutations from "mykrobe-style" files. mutation_to_drug_json is json file
of mutation -> list of drugs. variants_txt is text file of variants used my mykrobe's
make probes. gene_coords should be dict of gene coords made by the function
genbank_to_gene_coords'''
with open(mutation_to_drug_json) as f:
drug_data = json.load(f)
mutations = []
genes_with_indels = set()
genes_need_upstream = set()
genes_non_upstream = set()
with open(variants_txt) as f:
for line in f:
gene, variant, d_or_p = line.rstrip().split('\t')
coding = 0 if gene == 'rrs' else 1
d = {'gene': gene, 'var': variant, 'coding': coding, 'upstream': False}
drug_data_key = d['gene'] + '_' + d['var']
if drug_data_key not in drug_data:
print('KEY', drug_data_key, 'NOT FOUND', file=sys.stderr)
else:
d['drugs'] = ','.join(sorted(drug_data[drug_data_key]))
if d_or_p == 'DNA' and gene != 'rrs':
assert gene != 'rrs'
re_match = re.match('([ACGT]+)(-?[0-9]+)([ACGTX]+)', d['var'])
try:
ref, pos, alt = re_match.groups()
except:
print('regex error:', d['var'], file=sys.stderr)
continue
pos = int(pos)
if len(ref) != len(alt):
genes_with_indels.add(d['gene'])
continue
elif pos > 0:
#print('ignoring synonymous change (not implemented):', d['gene'], d['var'], d['drugs'], file=sys.stderr)
continue
elif pos < 0:
this_gene_coords = gene_coords[d['gene']]
d['upstream'] = True
if this_gene_coords['start'] < this_gene_coords['end']:
variant_pos_in_output_seq = upstream_before + pos + 1
else:
variant_pos_in_output_seq = upstream_before + pos + 1
assert variant_pos_in_output_seq > 0
d['var'] = ref + str(variant_pos_in_output_seq) + alt
d['original_mutation'] = variant
genes_need_upstream.add(d['gene'])
elif pos == 0:
print('Zero coord!', d, file=sys.stderr)
continue
else:
print('deal with?', d, file=sys.stderr)
continue
mutations.append(d)
if not d['upstream']:
genes_non_upstream.add(d['gene'])
return mutations, genes_with_indels, genes_need_upstream, genes_non_upstream | python | def load_mutations(gene_coords, mutation_to_drug_json, variants_txt, upstream_before=100):
'''Load mutations from "mykrobe-style" files. mutation_to_drug_json is json file
of mutation -> list of drugs. variants_txt is text file of variants used my mykrobe's
make probes. gene_coords should be dict of gene coords made by the function
genbank_to_gene_coords'''
with open(mutation_to_drug_json) as f:
drug_data = json.load(f)
mutations = []
genes_with_indels = set()
genes_need_upstream = set()
genes_non_upstream = set()
with open(variants_txt) as f:
for line in f:
gene, variant, d_or_p = line.rstrip().split('\t')
coding = 0 if gene == 'rrs' else 1
d = {'gene': gene, 'var': variant, 'coding': coding, 'upstream': False}
drug_data_key = d['gene'] + '_' + d['var']
if drug_data_key not in drug_data:
print('KEY', drug_data_key, 'NOT FOUND', file=sys.stderr)
else:
d['drugs'] = ','.join(sorted(drug_data[drug_data_key]))
if d_or_p == 'DNA' and gene != 'rrs':
assert gene != 'rrs'
re_match = re.match('([ACGT]+)(-?[0-9]+)([ACGTX]+)', d['var'])
try:
ref, pos, alt = re_match.groups()
except:
print('regex error:', d['var'], file=sys.stderr)
continue
pos = int(pos)
if len(ref) != len(alt):
genes_with_indels.add(d['gene'])
continue
elif pos > 0:
#print('ignoring synonymous change (not implemented):', d['gene'], d['var'], d['drugs'], file=sys.stderr)
continue
elif pos < 0:
this_gene_coords = gene_coords[d['gene']]
d['upstream'] = True
if this_gene_coords['start'] < this_gene_coords['end']:
variant_pos_in_output_seq = upstream_before + pos + 1
else:
variant_pos_in_output_seq = upstream_before + pos + 1
assert variant_pos_in_output_seq > 0
d['var'] = ref + str(variant_pos_in_output_seq) + alt
d['original_mutation'] = variant
genes_need_upstream.add(d['gene'])
elif pos == 0:
print('Zero coord!', d, file=sys.stderr)
continue
else:
print('deal with?', d, file=sys.stderr)
continue
mutations.append(d)
if not d['upstream']:
genes_non_upstream.add(d['gene'])
return mutations, genes_with_indels, genes_need_upstream, genes_non_upstream | [
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of mutation -> list of drugs. variants_txt is text file of variants used my mykrobe's
make probes. gene_coords should be dict of gene coords made by the function
genbank_to_gene_coords | [
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2,206 | sanger-pathogens/ariba | ariba/tb.py | write_prepareref_fasta_file | def write_prepareref_fasta_file(outfile, gene_coords, genes_need_upstream, genes_non_upstream, upstream_before=100, upstream_after=100):
'''Writes fasta file to be used with -f option of prepareref'''
tmp_dict = {}
fasta_in = os.path.join(data_dir, 'NC_000962.3.fa.gz')
pyfastaq.tasks.file_to_dict(fasta_in, tmp_dict)
ref_seq = tmp_dict['NC_000962.3']
with open(outfile, 'w') as f:
for gene in genes_non_upstream:
start = gene_coords[gene]['start']
end = gene_coords[gene]['end']
if start < end:
gene_fa = pyfastaq.sequences.Fasta(gene, ref_seq[start:end+1])
else:
gene_fa = pyfastaq.sequences.Fasta(gene, ref_seq[end:start+1])
gene_fa.revcomp()
print(gene_fa, file=f)
for gene in genes_need_upstream:
start = gene_coords[gene]['start']
end = gene_coords[gene]['end']
if start < end:
gene_fa = pyfastaq.sequences.Fasta(gene, ref_seq[start - upstream_before:start + upstream_after])
else:
gene_fa = pyfastaq.sequences.Fasta(gene, ref_seq[start - upstream_after + 1:start + upstream_before + 1])
gene_fa.revcomp()
gene_fa.id += '_upstream'
print(gene_fa, file=f) | python | def write_prepareref_fasta_file(outfile, gene_coords, genes_need_upstream, genes_non_upstream, upstream_before=100, upstream_after=100):
'''Writes fasta file to be used with -f option of prepareref'''
tmp_dict = {}
fasta_in = os.path.join(data_dir, 'NC_000962.3.fa.gz')
pyfastaq.tasks.file_to_dict(fasta_in, tmp_dict)
ref_seq = tmp_dict['NC_000962.3']
with open(outfile, 'w') as f:
for gene in genes_non_upstream:
start = gene_coords[gene]['start']
end = gene_coords[gene]['end']
if start < end:
gene_fa = pyfastaq.sequences.Fasta(gene, ref_seq[start:end+1])
else:
gene_fa = pyfastaq.sequences.Fasta(gene, ref_seq[end:start+1])
gene_fa.revcomp()
print(gene_fa, file=f)
for gene in genes_need_upstream:
start = gene_coords[gene]['start']
end = gene_coords[gene]['end']
if start < end:
gene_fa = pyfastaq.sequences.Fasta(gene, ref_seq[start - upstream_before:start + upstream_after])
else:
gene_fa = pyfastaq.sequences.Fasta(gene, ref_seq[start - upstream_after + 1:start + upstream_before + 1])
gene_fa.revcomp()
gene_fa.id += '_upstream'
print(gene_fa, file=f) | [
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2,207 | sanger-pathogens/ariba | ariba/summary_cluster.py | SummaryCluster._get_known_noncoding_het_snp | def _get_known_noncoding_het_snp(data_dict):
'''If ref is coding, return None. If the data dict has a known snp, and
samtools made a call, then return the string ref_name_change and the
% of reads supporting the variant type. If noncoding, but no
samtools call, then return None'''
if data_dict['gene'] == '1':
return None
if data_dict['known_var'] == '1' and data_dict['ref_ctg_effect'] == 'SNP' \
and data_dict['smtls_nts'] != '.' and ';' not in data_dict['smtls_nts']:
nucleotides = data_dict['smtls_nts'].split(',')
depths = data_dict['smtls_nts_depth'].split(',')
if len(nucleotides) != len(depths):
raise Error('Mismatch in number of inferred nucleotides from ctg_nt, smtls_nts, smtls_nts_depth columns. Cannot continue\n' + str(data_dict))
try:
var_nucleotide = data_dict['known_var_change'][-1]
depths = [int(x) for x in depths]
nuc_to_depth = dict(zip(nucleotides, depths))
total_depth = sum(depths)
var_depth = nuc_to_depth.get(var_nucleotide, 0)
percent_depth = round(100 * var_depth / total_depth, 1)
except:
return None
return data_dict['known_var_change'], percent_depth
else:
return None | python | def _get_known_noncoding_het_snp(data_dict):
'''If ref is coding, return None. If the data dict has a known snp, and
samtools made a call, then return the string ref_name_change and the
% of reads supporting the variant type. If noncoding, but no
samtools call, then return None'''
if data_dict['gene'] == '1':
return None
if data_dict['known_var'] == '1' and data_dict['ref_ctg_effect'] == 'SNP' \
and data_dict['smtls_nts'] != '.' and ';' not in data_dict['smtls_nts']:
nucleotides = data_dict['smtls_nts'].split(',')
depths = data_dict['smtls_nts_depth'].split(',')
if len(nucleotides) != len(depths):
raise Error('Mismatch in number of inferred nucleotides from ctg_nt, smtls_nts, smtls_nts_depth columns. Cannot continue\n' + str(data_dict))
try:
var_nucleotide = data_dict['known_var_change'][-1]
depths = [int(x) for x in depths]
nuc_to_depth = dict(zip(nucleotides, depths))
total_depth = sum(depths)
var_depth = nuc_to_depth.get(var_nucleotide, 0)
percent_depth = round(100 * var_depth / total_depth, 1)
except:
return None
return data_dict['known_var_change'], percent_depth
else:
return None | [
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samtools made a call, then return the string ref_name_change and the
% of reads supporting the variant type. If noncoding, but no
samtools call, then return None | [
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2,208 | sanger-pathogens/ariba | ariba/summary_cluster.py | SummaryCluster._has_match | def _has_match(self, assembled_summary):
'''assembled_summary should be output of _to_cluster_summary_assembled'''
if assembled_summary.startswith('yes'):
if self.data[0]['var_only'] == '0' or self._to_cluster_summary_has_known_nonsynonymous(assembled_summary) == 'yes':
return 'yes'
else:
return 'no'
else:
return 'no' | python | def _has_match(self, assembled_summary):
'''assembled_summary should be output of _to_cluster_summary_assembled'''
if assembled_summary.startswith('yes'):
if self.data[0]['var_only'] == '0' or self._to_cluster_summary_has_known_nonsynonymous(assembled_summary) == 'yes':
return 'yes'
else:
return 'no'
else:
return 'no' | [
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2,209 | sanger-pathogens/ariba | ariba/summary_cluster.py | SummaryCluster.has_var_groups | def has_var_groups(self):
'''Returns a set of the variant group ids that this cluster has'''
ids = set()
for d in self.data:
if self._has_known_variant(d) != 'no' and d['var_group'] != '.':
ids.add(d['var_group'])
return ids | python | def has_var_groups(self):
'''Returns a set of the variant group ids that this cluster has'''
ids = set()
for d in self.data:
if self._has_known_variant(d) != 'no' and d['var_group'] != '.':
ids.add(d['var_group'])
return ids | [
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2,210 | sanger-pathogens/ariba | ariba/summary_cluster.py | SummaryCluster.column_summary_data | def column_summary_data(self):
'''Returns a dictionary of column name -> value, for cluster-level results'''
assembled_summary = self._to_cluster_summary_assembled()
pct_id, read_depth = self._pc_id_and_read_depth_of_longest()
columns = {
'assembled': self._to_cluster_summary_assembled(),
'match': self._has_match(assembled_summary),
'ref_seq': self.ref_name,
'pct_id': str(pct_id),
'ctg_cov': str(read_depth),
'known_var': self._to_cluster_summary_has_known_nonsynonymous(assembled_summary),
'novel_var': self._to_cluster_summary_has_novel_nonsynonymous(assembled_summary)
}
return columns | python | def column_summary_data(self):
'''Returns a dictionary of column name -> value, for cluster-level results'''
assembled_summary = self._to_cluster_summary_assembled()
pct_id, read_depth = self._pc_id_and_read_depth_of_longest()
columns = {
'assembled': self._to_cluster_summary_assembled(),
'match': self._has_match(assembled_summary),
'ref_seq': self.ref_name,
'pct_id': str(pct_id),
'ctg_cov': str(read_depth),
'known_var': self._to_cluster_summary_has_known_nonsynonymous(assembled_summary),
'novel_var': self._to_cluster_summary_has_novel_nonsynonymous(assembled_summary)
}
return columns | [
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2,211 | sanger-pathogens/ariba | ariba/common.py | cat_files | def cat_files(infiles, outfile):
'''Cats all files in list infiles into outfile'''
f_out = pyfastaq.utils.open_file_write(outfile)
for filename in infiles:
if os.path.exists(filename):
f_in = pyfastaq.utils.open_file_read(filename)
for line in f_in:
print(line, end='', file=f_out)
pyfastaq.utils.close(f_in)
pyfastaq.utils.close(f_out) | python | def cat_files(infiles, outfile):
'''Cats all files in list infiles into outfile'''
f_out = pyfastaq.utils.open_file_write(outfile)
for filename in infiles:
if os.path.exists(filename):
f_in = pyfastaq.utils.open_file_read(filename)
for line in f_in:
print(line, end='', file=f_out)
pyfastaq.utils.close(f_in)
pyfastaq.utils.close(f_out) | [
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2,212 | sanger-pathogens/ariba | ariba/assembly.py | Assembly._check_spades_log_file | def _check_spades_log_file(logfile):
'''SPAdes can fail with a strange error. Stop everything if this happens'''
f = pyfastaq.utils.open_file_read(logfile)
for line in f:
if line.startswith('== Error == system call for:') and line.rstrip().endswith('finished abnormally, err code: -7'):
pyfastaq.utils.close(f)
print('Error running SPAdes. Cannot continue. This is the error from the log file', logfile, '...', file=sys.stderr)
print(line, file=sys.stderr)
raise Error('Fatal error ("err code: -7") running spades. Cannot continue')
pyfastaq.utils.close(f)
return True | python | def _check_spades_log_file(logfile):
'''SPAdes can fail with a strange error. Stop everything if this happens'''
f = pyfastaq.utils.open_file_read(logfile)
for line in f:
if line.startswith('== Error == system call for:') and line.rstrip().endswith('finished abnormally, err code: -7'):
pyfastaq.utils.close(f)
print('Error running SPAdes. Cannot continue. This is the error from the log file', logfile, '...', file=sys.stderr)
print(line, file=sys.stderr)
raise Error('Fatal error ("err code: -7") running spades. Cannot continue')
pyfastaq.utils.close(f)
return True | [
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2,213 | sanger-pathogens/ariba | ariba/assembly.py | Assembly._fix_contig_orientation | def _fix_contig_orientation(contigs_fa, ref_fa, outfile, min_id=90, min_length=20, breaklen=200):
'''Changes orientation of each contig to match the reference, when possible.
Returns a set of names of contigs that had hits in both orientations to the reference'''
if not os.path.exists(contigs_fa):
raise Error('Cannot fix orientation of assembly contigs because file not found: ' + contigs_fa)
tmp_coords = os.path.join(outfile + '.tmp.rename.coords')
pymummer.nucmer.Runner(
ref_fa,
contigs_fa,
tmp_coords,
min_id=min_id,
min_length=min_length,
breaklen=breaklen,
maxmatch=True,
).run()
to_revcomp = set()
not_revcomp = set()
file_reader = pymummer.coords_file.reader(tmp_coords)
for hit in file_reader:
if hit.on_same_strand():
not_revcomp.add(hit.qry_name)
else:
to_revcomp.add(hit.qry_name)
os.unlink(tmp_coords)
in_both = to_revcomp.intersection(not_revcomp)
f = pyfastaq.utils.open_file_write(outfile)
seq_reader = pyfastaq.sequences.file_reader(contigs_fa)
for seq in seq_reader:
if seq.id in to_revcomp and seq.id not in in_both:
seq.revcomp()
print(seq, file=f)
pyfastaq.utils.close(f)
return in_both | python | def _fix_contig_orientation(contigs_fa, ref_fa, outfile, min_id=90, min_length=20, breaklen=200):
'''Changes orientation of each contig to match the reference, when possible.
Returns a set of names of contigs that had hits in both orientations to the reference'''
if not os.path.exists(contigs_fa):
raise Error('Cannot fix orientation of assembly contigs because file not found: ' + contigs_fa)
tmp_coords = os.path.join(outfile + '.tmp.rename.coords')
pymummer.nucmer.Runner(
ref_fa,
contigs_fa,
tmp_coords,
min_id=min_id,
min_length=min_length,
breaklen=breaklen,
maxmatch=True,
).run()
to_revcomp = set()
not_revcomp = set()
file_reader = pymummer.coords_file.reader(tmp_coords)
for hit in file_reader:
if hit.on_same_strand():
not_revcomp.add(hit.qry_name)
else:
to_revcomp.add(hit.qry_name)
os.unlink(tmp_coords)
in_both = to_revcomp.intersection(not_revcomp)
f = pyfastaq.utils.open_file_write(outfile)
seq_reader = pyfastaq.sequences.file_reader(contigs_fa)
for seq in seq_reader:
if seq.id in to_revcomp and seq.id not in in_both:
seq.revcomp()
print(seq, file=f)
pyfastaq.utils.close(f)
return in_both | [
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Returns a set of names of contigs that had hits in both orientations to the reference | [
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2,214 | sanger-pathogens/ariba | ariba/assembly_compare.py | AssemblyCompare._parse_nucmer_coords_file | def _parse_nucmer_coords_file(coords_file, ref_name):
'''Input is coords file made by self._run_nucmer. Reference should have one sequence only.
ref_name is name fo the reference sequence, to sanity check the coords file.
Returns dictionary. Key = assembly contig name. Value = list of nucmer hits to that contig'''
file_reader = pymummer.coords_file.reader(coords_file)
nucmer_hits = {}
for hit in file_reader:
assert hit.ref_name == ref_name
contig = hit.qry_name
if contig not in nucmer_hits:
nucmer_hits[contig] = []
nucmer_hits[contig].append(copy.copy(hit))
return nucmer_hits | python | def _parse_nucmer_coords_file(coords_file, ref_name):
'''Input is coords file made by self._run_nucmer. Reference should have one sequence only.
ref_name is name fo the reference sequence, to sanity check the coords file.
Returns dictionary. Key = assembly contig name. Value = list of nucmer hits to that contig'''
file_reader = pymummer.coords_file.reader(coords_file)
nucmer_hits = {}
for hit in file_reader:
assert hit.ref_name == ref_name
contig = hit.qry_name
if contig not in nucmer_hits:
nucmer_hits[contig] = []
nucmer_hits[contig].append(copy.copy(hit))
return nucmer_hits | [
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2,215 | sanger-pathogens/ariba | ariba/assembly_compare.py | AssemblyCompare._nucmer_hits_to_percent_identity | def _nucmer_hits_to_percent_identity(nucmer_hits):
'''Input is hits made by self._parse_nucmer_coords_file.
Returns dictionary. key = contig name. Value = percent identity of hits to that contig'''
percent_identities = {}
max_lengths = {}
for contig in nucmer_hits:
max_length = -1
percent_identity = 0
for hit in nucmer_hits[contig]:
if hit.hit_length_qry > max_length:
max_length = hit.hit_length_qry
percent_identity = hit.percent_identity
percent_identities[contig] = percent_identity
return percent_identities | python | def _nucmer_hits_to_percent_identity(nucmer_hits):
'''Input is hits made by self._parse_nucmer_coords_file.
Returns dictionary. key = contig name. Value = percent identity of hits to that contig'''
percent_identities = {}
max_lengths = {}
for contig in nucmer_hits:
max_length = -1
percent_identity = 0
for hit in nucmer_hits[contig]:
if hit.hit_length_qry > max_length:
max_length = hit.hit_length_qry
percent_identity = hit.percent_identity
percent_identities[contig] = percent_identity
return percent_identities | [
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2,216 | sanger-pathogens/ariba | ariba/assembly_compare.py | AssemblyCompare._nucmer_hits_to_assembly_coords | def _nucmer_hits_to_assembly_coords(nucmer_hits):
'''Input is hits made by self._parse_nucmer_coords_file.
Returns dictionary. key = contig name. Value = list of coords that match
to the reference gene'''
coords = {}
for l in nucmer_hits.values():
for hit in l:
if hit.qry_name not in coords:
coords[hit.qry_name] = []
coords[hit.qry_name].append(hit.qry_coords())
for scaff in coords:
pyfastaq.intervals.merge_overlapping_in_list(coords[scaff])
return coords | python | def _nucmer_hits_to_assembly_coords(nucmer_hits):
'''Input is hits made by self._parse_nucmer_coords_file.
Returns dictionary. key = contig name. Value = list of coords that match
to the reference gene'''
coords = {}
for l in nucmer_hits.values():
for hit in l:
if hit.qry_name not in coords:
coords[hit.qry_name] = []
coords[hit.qry_name].append(hit.qry_coords())
for scaff in coords:
pyfastaq.intervals.merge_overlapping_in_list(coords[scaff])
return coords | [
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2,217 | sanger-pathogens/ariba | ariba/assembly_compare.py | AssemblyCompare.nucmer_hits_to_ref_coords | def nucmer_hits_to_ref_coords(cls, nucmer_hits, contig=None):
'''Input is hits made by self._parse_nucmer_coords_file.
Returns dictionary. Key = contig name. Value = list of coords in the
reference sequence for that contig.
if contig=contig_name, then just gets the ref coords from that contig,
instead of using all the contigs'''
coords = []
if contig is None:
coords = {key: [] for key in nucmer_hits.keys()}
else:
coords = {contig: []}
for key in coords:
coords[key] = [hit.ref_coords() for hit in nucmer_hits[key]]
pyfastaq.intervals.merge_overlapping_in_list(coords[key])
return coords | python | def nucmer_hits_to_ref_coords(cls, nucmer_hits, contig=None):
'''Input is hits made by self._parse_nucmer_coords_file.
Returns dictionary. Key = contig name. Value = list of coords in the
reference sequence for that contig.
if contig=contig_name, then just gets the ref coords from that contig,
instead of using all the contigs'''
coords = []
if contig is None:
coords = {key: [] for key in nucmer_hits.keys()}
else:
coords = {contig: []}
for key in coords:
coords[key] = [hit.ref_coords() for hit in nucmer_hits[key]]
pyfastaq.intervals.merge_overlapping_in_list(coords[key])
return coords | [
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2,218 | sanger-pathogens/ariba | ariba/assembly_compare.py | AssemblyCompare.nucmer_hits_to_ref_and_qry_coords | def nucmer_hits_to_ref_and_qry_coords(cls, nucmer_hits, contig=None):
'''Same as nucmer_hits_to_ref_coords, except removes containing hits first,
and returns ref and qry coords lists'''
if contig is None:
ctg_coords = {key: [] for key in nucmer_hits.keys()}
else:
ctg_coords = {contig: []}
ref_coords = {}
for key in ctg_coords:
hits = copy.copy(nucmer_hits[key])
hits.sort(key=lambda x: len(x.ref_coords()))
if len(hits) > 1:
i = 0
while i < len(hits) - 1:
c1 = hits[i].ref_coords()
c2 = hits[i+1].ref_coords()
if c2.contains(c1):
hits.pop(i)
else:
i += 1
ref_coords[key] = [hit.ref_coords() for hit in hits]
ctg_coords[key] = [hit.qry_coords() for hit in hits]
pyfastaq.intervals.merge_overlapping_in_list(ref_coords[key])
pyfastaq.intervals.merge_overlapping_in_list(ctg_coords[key])
return ctg_coords, ref_coords | python | def nucmer_hits_to_ref_and_qry_coords(cls, nucmer_hits, contig=None):
'''Same as nucmer_hits_to_ref_coords, except removes containing hits first,
and returns ref and qry coords lists'''
if contig is None:
ctg_coords = {key: [] for key in nucmer_hits.keys()}
else:
ctg_coords = {contig: []}
ref_coords = {}
for key in ctg_coords:
hits = copy.copy(nucmer_hits[key])
hits.sort(key=lambda x: len(x.ref_coords()))
if len(hits) > 1:
i = 0
while i < len(hits) - 1:
c1 = hits[i].ref_coords()
c2 = hits[i+1].ref_coords()
if c2.contains(c1):
hits.pop(i)
else:
i += 1
ref_coords[key] = [hit.ref_coords() for hit in hits]
ctg_coords[key] = [hit.qry_coords() for hit in hits]
pyfastaq.intervals.merge_overlapping_in_list(ref_coords[key])
pyfastaq.intervals.merge_overlapping_in_list(ctg_coords[key])
return ctg_coords, ref_coords | [
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2,219 | sanger-pathogens/ariba | ariba/assembly_compare.py | AssemblyCompare.ref_cov_per_contig | def ref_cov_per_contig(nucmer_hits):
'''Input is hits made by self._parse_nucmer_coords_file.
Returns dictionary. key = contig name. Value = number of bases that
match to the reference sequence.'''
coords = AssemblyCompare.nucmer_hits_to_ref_coords(nucmer_hits)
return {x: pyfastaq.intervals.length_sum_from_list(coords[x]) for x in coords} | python | def ref_cov_per_contig(nucmer_hits):
'''Input is hits made by self._parse_nucmer_coords_file.
Returns dictionary. key = contig name. Value = number of bases that
match to the reference sequence.'''
coords = AssemblyCompare.nucmer_hits_to_ref_coords(nucmer_hits)
return {x: pyfastaq.intervals.length_sum_from_list(coords[x]) for x in coords} | [
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2,220 | sanger-pathogens/ariba | ariba/assembly_compare.py | AssemblyCompare._ref_covered_by_at_least_one_full_length_contig | def _ref_covered_by_at_least_one_full_length_contig(nucmer_hits, percent_threshold, max_nt_extend):
'''Returns true iff there exists a contig that completely
covers the reference sequence
nucmer_hits = hits made by self._parse_nucmer_coords_file.'''
for l in nucmer_hits.values():
for hit in l:
if ( (2 * max_nt_extend) + len(hit.ref_coords()) ) / hit.ref_length >= percent_threshold:
return True
return False | python | def _ref_covered_by_at_least_one_full_length_contig(nucmer_hits, percent_threshold, max_nt_extend):
'''Returns true iff there exists a contig that completely
covers the reference sequence
nucmer_hits = hits made by self._parse_nucmer_coords_file.'''
for l in nucmer_hits.values():
for hit in l:
if ( (2 * max_nt_extend) + len(hit.ref_coords()) ) / hit.ref_length >= percent_threshold:
return True
return False | [
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2,221 | sanger-pathogens/ariba | ariba/assembly_compare.py | AssemblyCompare.nucmer_hit_containing_reference_position | def nucmer_hit_containing_reference_position(nucmer_hits, ref_name, ref_position, qry_name=None):
'''Returns the first nucmer match found that contains the given
reference location. nucmer_hits = hits made by self._parse_nucmer_coords_file.
Returns None if no matching hit found'''
for contig_name in nucmer_hits:
for hit in nucmer_hits[contig_name]:
if hit.ref_name == ref_name and (qry_name is None or qry_name == hit.qry_name) and hit.ref_coords().distance_to_point(ref_position) == 0:
return hit
return None | python | def nucmer_hit_containing_reference_position(nucmer_hits, ref_name, ref_position, qry_name=None):
'''Returns the first nucmer match found that contains the given
reference location. nucmer_hits = hits made by self._parse_nucmer_coords_file.
Returns None if no matching hit found'''
for contig_name in nucmer_hits:
for hit in nucmer_hits[contig_name]:
if hit.ref_name == ref_name and (qry_name is None or qry_name == hit.qry_name) and hit.ref_coords().distance_to_point(ref_position) == 0:
return hit
return None | [
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2,222 | sanger-pathogens/ariba | ariba/external_progs.py | ExternalProgs._get_exe | def _get_exe(prog):
'''Given a program name, return what we expect its exectuable to be called'''
if prog in prog_to_env_var:
env_var = prog_to_env_var[prog]
if env_var in os.environ:
return os.environ[env_var]
return prog_to_default[prog] | python | def _get_exe(prog):
'''Given a program name, return what we expect its exectuable to be called'''
if prog in prog_to_env_var:
env_var = prog_to_env_var[prog]
if env_var in os.environ:
return os.environ[env_var]
return prog_to_default[prog] | [
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2,223 | sanger-pathogens/ariba | ariba/cdhit.py | Runner.fake_run | def fake_run(self):
'''Doesn't actually run cd-hit. Instead, puts each input sequence into its own cluster. So it's as if cdhit was run, but didn't cluster anything'''
clusters = {}
used_names = set()
seq_reader = pyfastaq.sequences.file_reader(self.infile)
for seq in seq_reader:
if seq.id in used_names:
raise Error('Sequence name "' + seq.id + '" not unique. Cannot continue')
clusters[str(len(clusters) + self.min_cluster_number)] = {seq.id}
used_names.add(seq.id)
return clusters | python | def fake_run(self):
'''Doesn't actually run cd-hit. Instead, puts each input sequence into its own cluster. So it's as if cdhit was run, but didn't cluster anything'''
clusters = {}
used_names = set()
seq_reader = pyfastaq.sequences.file_reader(self.infile)
for seq in seq_reader:
if seq.id in used_names:
raise Error('Sequence name "' + seq.id + '" not unique. Cannot continue')
clusters[str(len(clusters) + self.min_cluster_number)] = {seq.id}
used_names.add(seq.id)
return clusters | [
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2,224 | sanger-pathogens/ariba | ariba/cdhit.py | Runner.run_get_clusters_from_file | def run_get_clusters_from_file(self, clusters_infile, all_ref_seqs, rename_dict=None):
'''Instead of running cdhit, gets the clusters info from the input file.'''
if rename_dict is None:
rename_dict = {}
# check that every sequence in the clusters file can be
# found in the fasta file
seq_reader = pyfastaq.sequences.file_reader(self.infile)
names_list_from_fasta_file = [seq.id for seq in seq_reader]
names_set_from_fasta_file = set(names_list_from_fasta_file)
clusters = self._load_user_clusters_file(clusters_infile, all_ref_seqs, rename_dict=rename_dict)
if len(names_set_from_fasta_file) != len(names_list_from_fasta_file):
raise Error('At least one duplicate name in fasta file ' + self.infile + '. Cannot continue')
names_from_clusters_file = set()
for new_names in clusters.values():
names_from_clusters_file.update(new_names)
if not names_set_from_fasta_file.issubset(names_from_clusters_file):
raise Error('Some names in fasta file "' + self.infile + '" not given in cluster file. Cannot continue')
return clusters | python | def run_get_clusters_from_file(self, clusters_infile, all_ref_seqs, rename_dict=None):
'''Instead of running cdhit, gets the clusters info from the input file.'''
if rename_dict is None:
rename_dict = {}
# check that every sequence in the clusters file can be
# found in the fasta file
seq_reader = pyfastaq.sequences.file_reader(self.infile)
names_list_from_fasta_file = [seq.id for seq in seq_reader]
names_set_from_fasta_file = set(names_list_from_fasta_file)
clusters = self._load_user_clusters_file(clusters_infile, all_ref_seqs, rename_dict=rename_dict)
if len(names_set_from_fasta_file) != len(names_list_from_fasta_file):
raise Error('At least one duplicate name in fasta file ' + self.infile + '. Cannot continue')
names_from_clusters_file = set()
for new_names in clusters.values():
names_from_clusters_file.update(new_names)
if not names_set_from_fasta_file.issubset(names_from_clusters_file):
raise Error('Some names in fasta file "' + self.infile + '" not given in cluster file. Cannot continue')
return clusters | [
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2,225 | sanger-pathogens/ariba | ariba/mapping.py | sam_pair_to_insert | def sam_pair_to_insert(s1, s2):
'''Returns insert size from pair of sam records, as long as their orientation is "innies".
Otherwise returns None.'''
if s1.is_unmapped or s2.is_unmapped or (s1.tid != s2.tid) or (s1.is_reverse == s2.is_reverse):
return None
# If here, reads are both mapped to the same ref, and in opposite orientations
if s1.is_reverse:
end = s1.reference_end - 1
start = s2.reference_start
else:
end = s2.reference_end - 1
start = s1.reference_start
if start < end:
return end - start + 1
else:
return None | python | def sam_pair_to_insert(s1, s2):
'''Returns insert size from pair of sam records, as long as their orientation is "innies".
Otherwise returns None.'''
if s1.is_unmapped or s2.is_unmapped or (s1.tid != s2.tid) or (s1.is_reverse == s2.is_reverse):
return None
# If here, reads are both mapped to the same ref, and in opposite orientations
if s1.is_reverse:
end = s1.reference_end - 1
start = s2.reference_start
else:
end = s2.reference_end - 1
start = s1.reference_start
if start < end:
return end - start + 1
else:
return None | [
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2,226 | sanger-pathogens/ariba | ariba/scaffold_graph.py | Graph.update_from_sam | def update_from_sam(self, sam, sam_reader):
'''Updates graph info from a pysam.AlignedSegment object'''
if sam.is_unmapped \
or sam.mate_is_unmapped \
or (sam.reference_id == sam.next_reference_id):
return
new_link = link.Link(sam, sam_reader, self.ref_lengths)
read_name = sam.query_name
if read_name in self.partial_links:
new_link.merge(self.partial_links[read_name])
del self.partial_links[read_name]
key = tuple(sorted((new_link.refnames[0], new_link.refnames[1])))
if key not in self.links:
self.links[key] = []
new_link.sort()
self.links[key].append(new_link)
else:
self.partial_links[read_name] = new_link | python | def update_from_sam(self, sam, sam_reader):
'''Updates graph info from a pysam.AlignedSegment object'''
if sam.is_unmapped \
or sam.mate_is_unmapped \
or (sam.reference_id == sam.next_reference_id):
return
new_link = link.Link(sam, sam_reader, self.ref_lengths)
read_name = sam.query_name
if read_name in self.partial_links:
new_link.merge(self.partial_links[read_name])
del self.partial_links[read_name]
key = tuple(sorted((new_link.refnames[0], new_link.refnames[1])))
if key not in self.links:
self.links[key] = []
new_link.sort()
self.links[key].append(new_link)
else:
self.partial_links[read_name] = new_link | [
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2,227 | sanger-pathogens/ariba | ariba/scaffold_graph.py | Graph._make_graph | def _make_graph(self, max_insert):
'''helper function to construct graph from current state of object'''
if len(self.partial_links) != 0:
raise Error('Error in _make_graph(). Cannot continue because there are partial links')
self.contig_links = {}
for key in self.links:
for l in self.links[key]:
insert_size = l.insert_size()
if insert_size <= max_insert:
if key not in self.contig_links:
self.contig_links[key] = {}
dirs = ''.join(l.dirs)
self.contig_links[key][dirs] = self.contig_links[key].get(dirs, 0) + 1 | python | def _make_graph(self, max_insert):
'''helper function to construct graph from current state of object'''
if len(self.partial_links) != 0:
raise Error('Error in _make_graph(). Cannot continue because there are partial links')
self.contig_links = {}
for key in self.links:
for l in self.links[key]:
insert_size = l.insert_size()
if insert_size <= max_insert:
if key not in self.contig_links:
self.contig_links[key] = {}
dirs = ''.join(l.dirs)
self.contig_links[key][dirs] = self.contig_links[key].get(dirs, 0) + 1 | [
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2,228 | sanger-pathogens/ariba | ariba/bam_parse.py | Parser._sam_to_soft_clipped | def _sam_to_soft_clipped(self, sam):
'''Returns tuple of whether or not the left and right end of the mapped read in the sam record is soft-clipped'''
if sam.is_unmapped:
raise Error('Cannot get soft clip info from an unmapped read')
if sam.cigar is None or len(sam.cigar) == 0:
return False, False
return (sam.cigar[0][0] == 4, sam.cigar[-1][0] == 4) | python | def _sam_to_soft_clipped(self, sam):
'''Returns tuple of whether or not the left and right end of the mapped read in the sam record is soft-clipped'''
if sam.is_unmapped:
raise Error('Cannot get soft clip info from an unmapped read')
if sam.cigar is None or len(sam.cigar) == 0:
return False, False
return (sam.cigar[0][0] == 4, sam.cigar[-1][0] == 4) | [
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2,229 | sanger-pathogens/ariba | ariba/report_filter.py | ReportFilter._report_line_to_dict | def _report_line_to_dict(cls, line):
'''Takes report line string as input. Returns a dict of column name -> value in line'''
data = line.split('\t')
if len(data) != len(report.columns):
return None
d = dict(zip(report.columns, data))
for key in report.int_columns:
try:
d[key] = int(d[key])
except:
assert d[key] == '.'
for key in report.float_columns:
try:
d[key] = float(d[key])
except:
assert d[key] == '.'
d['flag'] = flag.Flag(int(d['flag']))
return d | python | def _report_line_to_dict(cls, line):
'''Takes report line string as input. Returns a dict of column name -> value in line'''
data = line.split('\t')
if len(data) != len(report.columns):
return None
d = dict(zip(report.columns, data))
for key in report.int_columns:
try:
d[key] = int(d[key])
except:
assert d[key] == '.'
for key in report.float_columns:
try:
d[key] = float(d[key])
except:
assert d[key] == '.'
d['flag'] = flag.Flag(int(d['flag']))
return d | [
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2,230 | sanger-pathogens/ariba | ariba/report_filter.py | ReportFilter._dict_to_report_line | def _dict_to_report_line(cls, report_dict):
'''Takes a report_dict as input and returns a report line'''
return '\t'.join([str(report_dict[x]) for x in report.columns]) | python | def _dict_to_report_line(cls, report_dict):
'''Takes a report_dict as input and returns a report line'''
return '\t'.join([str(report_dict[x]) for x in report.columns]) | [
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2,231 | sanger-pathogens/ariba | ariba/report_filter.py | ReportFilter._load_report | def _load_report(infile):
'''Loads report file into a dictionary. Key=reference name.
Value = list of report lines for that reference'''
report_dict = {}
f = pyfastaq.utils.open_file_read(infile)
first_line = True
for line in f:
line = line.rstrip()
if first_line:
expected_first_line = '#' + '\t'.join(report.columns)
if line != expected_first_line:
pyfastaq.utils.close(f)
raise Error('Error reading report file. Expected first line of file is\n' + expected_first_line + '\nbut got:\n' + line)
first_line = False
else:
line_dict = ReportFilter._report_line_to_dict(line)
if line_dict is None:
pyfastaq.utils.close(f)
raise Error('Error reading report file at this line:\n' + line)
ref_name = line_dict['ref_name']
ctg_name = line_dict['ctg']
if ref_name not in report_dict:
report_dict[ref_name] = {}
if ctg_name not in report_dict[ref_name]:
report_dict[ref_name][ctg_name] = []
report_dict[ref_name][ctg_name].append(line_dict)
pyfastaq.utils.close(f)
return report_dict | python | def _load_report(infile):
'''Loads report file into a dictionary. Key=reference name.
Value = list of report lines for that reference'''
report_dict = {}
f = pyfastaq.utils.open_file_read(infile)
first_line = True
for line in f:
line = line.rstrip()
if first_line:
expected_first_line = '#' + '\t'.join(report.columns)
if line != expected_first_line:
pyfastaq.utils.close(f)
raise Error('Error reading report file. Expected first line of file is\n' + expected_first_line + '\nbut got:\n' + line)
first_line = False
else:
line_dict = ReportFilter._report_line_to_dict(line)
if line_dict is None:
pyfastaq.utils.close(f)
raise Error('Error reading report file at this line:\n' + line)
ref_name = line_dict['ref_name']
ctg_name = line_dict['ctg']
if ref_name not in report_dict:
report_dict[ref_name] = {}
if ctg_name not in report_dict[ref_name]:
report_dict[ref_name][ctg_name] = []
report_dict[ref_name][ctg_name].append(line_dict)
pyfastaq.utils.close(f)
return report_dict | [
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2,232 | sanger-pathogens/ariba | ariba/report_filter.py | ReportFilter._filter_dicts | def _filter_dicts(self):
'''Filters out all the report_dicts that do not pass the cutoffs. If any ref sequence
loses all of its report_dicts, then it is completely removed.'''
keys_to_remove = set()
for ref_name in self.report:
for ctg_name in self.report[ref_name]:
self.report[ref_name][ctg_name] = self._filter_list_of_dicts(self.report[ref_name][ctg_name])
if len(self.report[ref_name][ctg_name]) == 0:
keys_to_remove.add((ref_name, ctg_name))
refs_to_remove = set()
for ref_name, ctg_name in keys_to_remove:
del self.report[ref_name][ctg_name]
if len(self.report[ref_name]) == 0:
refs_to_remove.add(ref_name)
for ref_name in refs_to_remove:
del self.report[ref_name] | python | def _filter_dicts(self):
'''Filters out all the report_dicts that do not pass the cutoffs. If any ref sequence
loses all of its report_dicts, then it is completely removed.'''
keys_to_remove = set()
for ref_name in self.report:
for ctg_name in self.report[ref_name]:
self.report[ref_name][ctg_name] = self._filter_list_of_dicts(self.report[ref_name][ctg_name])
if len(self.report[ref_name][ctg_name]) == 0:
keys_to_remove.add((ref_name, ctg_name))
refs_to_remove = set()
for ref_name, ctg_name in keys_to_remove:
del self.report[ref_name][ctg_name]
if len(self.report[ref_name]) == 0:
refs_to_remove.add(ref_name)
for ref_name in refs_to_remove:
del self.report[ref_name] | [
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2,233 | sanger-pathogens/ariba | ariba/link.py | Link.merge | def merge(self, other):
'''Merge another link into this one. Expected that each link was created from each mate from a pair. We only know both distances to contig ends when we have read info from both mappings in a BAM file. All other info should be the same.'''
assert self.refnames == other.refnames
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for i in range(2):
if self.pos[i] is None:
if other.pos[i] is None:
raise Error('Error merging these two links:\n' + str(self) + '\n' + str(other))
self.pos[i] = other.pos[i]
else:
if other.pos[i] is not None:
raise Error('Error merging these two links:\n' + str(self) + '\n' + str(other)) | python | def merge(self, other):
'''Merge another link into this one. Expected that each link was created from each mate from a pair. We only know both distances to contig ends when we have read info from both mappings in a BAM file. All other info should be the same.'''
assert self.refnames == other.refnames
assert self.dirs == other.dirs
assert self.lengths == other.lengths
for i in range(2):
if self.pos[i] is None:
if other.pos[i] is None:
raise Error('Error merging these two links:\n' + str(self) + '\n' + str(other))
self.pos[i] = other.pos[i]
else:
if other.pos[i] is not None:
raise Error('Error merging these two links:\n' + str(self) + '\n' + str(other)) | [
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2,234 | sanger-pathogens/ariba | ariba/summary.py | Summary._load_fofn | def _load_fofn(cls, fofn):
'''Returns dictionary of filename -> short name. Value is None
whenever short name is not provided'''
filenames = {}
f = pyfastaq.utils.open_file_read(fofn)
for line in f:
fields = line.rstrip().split()
if len(fields) == 1:
filenames[fields[0]] = None
elif len(fields) == 2:
filenames[fields[0]] = fields[1]
else:
raise Error('Error at the following line of file ' + fofn + '. Expected at most 2 fields.\n' + line)
pyfastaq.utils.close(f)
return filenames | python | def _load_fofn(cls, fofn):
'''Returns dictionary of filename -> short name. Value is None
whenever short name is not provided'''
filenames = {}
f = pyfastaq.utils.open_file_read(fofn)
for line in f:
fields = line.rstrip().split()
if len(fields) == 1:
filenames[fields[0]] = None
elif len(fields) == 2:
filenames[fields[0]] = fields[1]
else:
raise Error('Error at the following line of file ' + fofn + '. Expected at most 2 fields.\n' + line)
pyfastaq.utils.close(f)
return filenames | [
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2,235 | sanger-pathogens/ariba | ariba/summary.py | Summary._filter_matrix_rows | def _filter_matrix_rows(cls, matrix):
'''matrix = output from _to_matrix'''
indexes_to_keep = []
for i in range(len(matrix)):
keep_row = False
for element in matrix[i]:
if element not in {'NA', 'no'}:
keep_row = True
break
if keep_row:
indexes_to_keep.append(i)
return [matrix[i] for i in indexes_to_keep] | python | def _filter_matrix_rows(cls, matrix):
'''matrix = output from _to_matrix'''
indexes_to_keep = []
for i in range(len(matrix)):
keep_row = False
for element in matrix[i]:
if element not in {'NA', 'no'}:
keep_row = True
break
if keep_row:
indexes_to_keep.append(i)
return [matrix[i] for i in indexes_to_keep] | [
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2,236 | sanger-pathogens/ariba | ariba/summary.py | Summary._filter_matrix_columns | def _filter_matrix_columns(cls, matrix, phandango_header, csv_header):
'''phandango_header, csv_header, matrix = output from _to_matrix'''
indexes_to_keep = set()
for row in matrix:
for i in range(len(row)):
if row[i] not in {'NA', 'no'}:
indexes_to_keep.add(i)
indexes_to_keep = sorted(list(indexes_to_keep))
for i in range(len(matrix)):
matrix[i] = [matrix[i][j] for j in indexes_to_keep]
phandango_header = [phandango_header[i] for i in indexes_to_keep]
csv_header = [csv_header[i] for i in indexes_to_keep]
return phandango_header, csv_header, matrix | python | def _filter_matrix_columns(cls, matrix, phandango_header, csv_header):
'''phandango_header, csv_header, matrix = output from _to_matrix'''
indexes_to_keep = set()
for row in matrix:
for i in range(len(row)):
if row[i] not in {'NA', 'no'}:
indexes_to_keep.add(i)
indexes_to_keep = sorted(list(indexes_to_keep))
for i in range(len(matrix)):
matrix[i] = [matrix[i][j] for j in indexes_to_keep]
phandango_header = [phandango_header[i] for i in indexes_to_keep]
csv_header = [csv_header[i] for i in indexes_to_keep]
return phandango_header, csv_header, matrix | [
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2,237 | sanger-pathogens/ariba | ariba/assembly_variants.py | AssemblyVariants._get_remaining_known_ref_variants | def _get_remaining_known_ref_variants(known_ref_variants, used_ref_variants, nucmer_coords):
'''Finds variants where ref has the variant and so does the contig. Which means
that there was no mummer call to flag it up so need to look through the known
ref variants. Also need to check that the variant is in a nucmer match to an
assembly contig.'''
variants = []
for ref_variant_pos, ref_variants_set in sorted(known_ref_variants.items()):
for known_ref_variant in ref_variants_set:
if known_ref_variant not in used_ref_variants:
variant_pos_matches_contig = False
pos = known_ref_variant.variant.position
if known_ref_variant.seq_type == 'n':
ref_interval = intervals.Interval(pos, pos)
elif known_ref_variant.seq_type == 'p':
ref_interval = intervals.Interval(3 * pos, 3 * pos + 2)
else:
raise Error('Unexpected variant type "' + known_ref_variant.variant_type + '" in _get_remaining_known_ref_variants. Cannot continue')
for interval in nucmer_coords:
if ref_interval.intersects(interval):
variant_pos_matches_contig = True
break
if variant_pos_matches_contig:
variants.append((None, known_ref_variant.seq_type, None, None, None, {known_ref_variant}, set()))
return variants | python | def _get_remaining_known_ref_variants(known_ref_variants, used_ref_variants, nucmer_coords):
'''Finds variants where ref has the variant and so does the contig. Which means
that there was no mummer call to flag it up so need to look through the known
ref variants. Also need to check that the variant is in a nucmer match to an
assembly contig.'''
variants = []
for ref_variant_pos, ref_variants_set in sorted(known_ref_variants.items()):
for known_ref_variant in ref_variants_set:
if known_ref_variant not in used_ref_variants:
variant_pos_matches_contig = False
pos = known_ref_variant.variant.position
if known_ref_variant.seq_type == 'n':
ref_interval = intervals.Interval(pos, pos)
elif known_ref_variant.seq_type == 'p':
ref_interval = intervals.Interval(3 * pos, 3 * pos + 2)
else:
raise Error('Unexpected variant type "' + known_ref_variant.variant_type + '" in _get_remaining_known_ref_variants. Cannot continue')
for interval in nucmer_coords:
if ref_interval.intersects(interval):
variant_pos_matches_contig = True
break
if variant_pos_matches_contig:
variants.append((None, known_ref_variant.seq_type, None, None, None, {known_ref_variant}, set()))
return variants | [
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ref variants. Also need to check that the variant is in a nucmer match to an
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2,238 | sanger-pathogens/ariba | ariba/report.py | _samtools_depths_at_known_snps_all_wild | def _samtools_depths_at_known_snps_all_wild(sequence_meta, contig_name, cluster, variant_list):
'''Input is a known variants, as sequence_metadata object. The
assumption is that both the reference and the assembly have the
variant type, not wild type. The list variant_list should be a list
of pymummer.variant.Variant objects, only contaning variants to the
relevant query contig'''
ref_nuc_range = sequence_meta.variant.nucleotide_range()
if ref_nuc_range is None:
return None
bases = []
ctg_nts = []
ref_nts = []
smtls_total_depths = []
smtls_nts = []
smtls_depths = []
contig_positions = []
for ref_position in range(ref_nuc_range[0], ref_nuc_range[1]+1, 1):
nucmer_match = cluster.assembly_compare.nucmer_hit_containing_reference_position(cluster.assembly_compare.nucmer_hits, cluster.ref_sequence.id, ref_position, qry_name=contig_name)
if nucmer_match is not None:
# work out contig position. Needs indels variants to correct the position
ref_nts.append(cluster.ref_sequence[ref_position])
contig_position, in_indel = nucmer_match.qry_coords_from_ref_coord(ref_position, variant_list)
contig_positions.append(contig_position)
bases, total_depth, base_depths = cluster.samtools_vars.get_depths_at_position(contig_name, contig_position)
ctg_nts.append(cluster.assembly.sequences[contig_name][contig_position])
smtls_nts.append(bases)
smtls_total_depths.append(total_depth)
smtls_depths.append(base_depths)
ctg_nts = ';'.join(ctg_nts) if len(ctg_nts) else '.'
ref_nts = ';'.join(ref_nts) if len(ref_nts) else '.'
smtls_nts = ';'.join(smtls_nts) if len(smtls_nts) else '.'
smtls_total_depths = ';'.join([str(x)for x in smtls_total_depths]) if len(smtls_total_depths) else '.'
smtls_depths = ';'.join([str(x)for x in smtls_depths]) if len(smtls_depths) else '.'
ctg_start = str(min(contig_positions) + 1) if contig_positions is not None else '.'
ctg_end = str(max(contig_positions) + 1) if contig_positions is not None else '.'
return [str(x) for x in [
ref_nuc_range[0] + 1,
ref_nuc_range[1] + 1,
ref_nts,
ctg_start,
ctg_end,
ctg_nts,
smtls_total_depths,
smtls_nts,
smtls_depths
]] | python | def _samtools_depths_at_known_snps_all_wild(sequence_meta, contig_name, cluster, variant_list):
'''Input is a known variants, as sequence_metadata object. The
assumption is that both the reference and the assembly have the
variant type, not wild type. The list variant_list should be a list
of pymummer.variant.Variant objects, only contaning variants to the
relevant query contig'''
ref_nuc_range = sequence_meta.variant.nucleotide_range()
if ref_nuc_range is None:
return None
bases = []
ctg_nts = []
ref_nts = []
smtls_total_depths = []
smtls_nts = []
smtls_depths = []
contig_positions = []
for ref_position in range(ref_nuc_range[0], ref_nuc_range[1]+1, 1):
nucmer_match = cluster.assembly_compare.nucmer_hit_containing_reference_position(cluster.assembly_compare.nucmer_hits, cluster.ref_sequence.id, ref_position, qry_name=contig_name)
if nucmer_match is not None:
# work out contig position. Needs indels variants to correct the position
ref_nts.append(cluster.ref_sequence[ref_position])
contig_position, in_indel = nucmer_match.qry_coords_from_ref_coord(ref_position, variant_list)
contig_positions.append(contig_position)
bases, total_depth, base_depths = cluster.samtools_vars.get_depths_at_position(contig_name, contig_position)
ctg_nts.append(cluster.assembly.sequences[contig_name][contig_position])
smtls_nts.append(bases)
smtls_total_depths.append(total_depth)
smtls_depths.append(base_depths)
ctg_nts = ';'.join(ctg_nts) if len(ctg_nts) else '.'
ref_nts = ';'.join(ref_nts) if len(ref_nts) else '.'
smtls_nts = ';'.join(smtls_nts) if len(smtls_nts) else '.'
smtls_total_depths = ';'.join([str(x)for x in smtls_total_depths]) if len(smtls_total_depths) else '.'
smtls_depths = ';'.join([str(x)for x in smtls_depths]) if len(smtls_depths) else '.'
ctg_start = str(min(contig_positions) + 1) if contig_positions is not None else '.'
ctg_end = str(max(contig_positions) + 1) if contig_positions is not None else '.'
return [str(x) for x in [
ref_nuc_range[0] + 1,
ref_nuc_range[1] + 1,
ref_nts,
ctg_start,
ctg_end,
ctg_nts,
smtls_total_depths,
smtls_nts,
smtls_depths
]] | [
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] | 16a0b1916ce0e886bd22550ba2d648542977001b | https://github.com/sanger-pathogens/ariba/blob/16a0b1916ce0e886bd22550ba2d648542977001b/ariba/report.py#L85-L136 |
2,239 | ethereum/eth-abi | eth_abi/utils/string.py | abbr | def abbr(value: Any, limit: int=20) -> str:
"""
Converts a value into its string representation and abbreviates that
representation based on the given length `limit` if necessary.
"""
rep = repr(value)
if len(rep) > limit:
if limit < 3:
raise ValueError('Abbreviation limit may not be less than 3')
rep = rep[:limit - 3] + '...'
return rep | python | def abbr(value: Any, limit: int=20) -> str:
"""
Converts a value into its string representation and abbreviates that
representation based on the given length `limit` if necessary.
"""
rep = repr(value)
if len(rep) > limit:
if limit < 3:
raise ValueError('Abbreviation limit may not be less than 3')
rep = rep[:limit - 3] + '...'
return rep | [
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2,240 | ethereum/eth-abi | eth_abi/encoding.py | BaseEncoder.invalidate_value | def invalidate_value(
cls,
value: Any,
exc: Type[Exception]=EncodingTypeError,
msg: Optional[str]=None,
) -> None:
"""
Throws a standard exception for when a value is not encodable by an
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"""
raise exc(
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rep=abbr(value),
typ=type(value),
cls=cls.__name__,
msg="" if msg is None else (": " + msg),
)
) | python | def invalidate_value(
cls,
value: Any,
exc: Type[Exception]=EncodingTypeError,
msg: Optional[str]=None,
) -> None:
"""
Throws a standard exception for when a value is not encodable by an
encoder.
"""
raise exc(
"Value `{rep}` of type {typ} cannot be encoded by {cls}{msg}".format(
rep=abbr(value),
typ=type(value),
cls=cls.__name__,
msg="" if msg is None else (": " + msg),
)
) | [
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2,241 | ethereum/eth-abi | eth_abi/base.py | parse_tuple_type_str | def parse_tuple_type_str(old_from_type_str):
"""
Used by BaseCoder subclasses as a convenience for implementing the
``from_type_str`` method required by ``ABIRegistry``. Useful if normalizing
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"""
@functools.wraps(old_from_type_str)
def new_from_type_str(cls, type_str, registry):
normalized_type_str = normalize(type_str)
abi_type = parse(normalized_type_str)
type_str_repr = repr(type_str)
if type_str != normalized_type_str:
type_str_repr = '{} (normalized to {})'.format(
type_str_repr,
repr(normalized_type_str),
)
if not isinstance(abi_type, TupleType):
raise ValueError(
'Cannot create {} for non-tuple type {}'.format(
cls.__name__,
type_str_repr,
)
)
abi_type.validate()
return old_from_type_str(cls, abi_type, registry)
return classmethod(new_from_type_str) | python | def parse_tuple_type_str(old_from_type_str):
"""
Used by BaseCoder subclasses as a convenience for implementing the
``from_type_str`` method required by ``ABIRegistry``. Useful if normalizing
then parsing a tuple type string is required in that method.
"""
@functools.wraps(old_from_type_str)
def new_from_type_str(cls, type_str, registry):
normalized_type_str = normalize(type_str)
abi_type = parse(normalized_type_str)
type_str_repr = repr(type_str)
if type_str != normalized_type_str:
type_str_repr = '{} (normalized to {})'.format(
type_str_repr,
repr(normalized_type_str),
)
if not isinstance(abi_type, TupleType):
raise ValueError(
'Cannot create {} for non-tuple type {}'.format(
cls.__name__,
type_str_repr,
)
)
abi_type.validate()
return old_from_type_str(cls, abi_type, registry)
return classmethod(new_from_type_str) | [
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2,242 | ethereum/eth-abi | eth_abi/decoding.py | ContextFramesBytesIO.seek_in_frame | def seek_in_frame(self, pos, *args, **kwargs):
"""
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"""
super().seek(self._total_offset + pos, *args, **kwargs) | python | def seek_in_frame(self, pos, *args, **kwargs):
"""
Seeks relative to the total offset of the current contextual frames.
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2,243 | ethereum/eth-abi | eth_abi/decoding.py | ContextFramesBytesIO.push_frame | def push_frame(self, offset):
"""
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total offset.
"""
self._frames.append((offset, self.tell()))
self._total_offset += offset
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"""
Pushes a new contextual frame onto the stack with the given offset and a
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total offset.
"""
self._frames.append((offset, self.tell()))
self._total_offset += offset
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2,244 | ethereum/eth-abi | eth_abi/decoding.py | ContextFramesBytesIO.pop_frame | def pop_frame(self):
"""
Pops the current contextual frame off of the stack and returns the
cursor to the frame's return position.
"""
try:
offset, return_pos = self._frames.pop()
except IndexError:
raise IndexError('no frames to pop')
self._total_offset -= offset
self.seek(return_pos) | python | def pop_frame(self):
"""
Pops the current contextual frame off of the stack and returns the
cursor to the frame's return position.
"""
try:
offset, return_pos = self._frames.pop()
except IndexError:
raise IndexError('no frames to pop')
self._total_offset -= offset
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2,245 | ethereum/eth-abi | eth_abi/registry.py | has_arrlist | def has_arrlist(type_str):
"""
A predicate that matches a type string with an array dimension list.
"""
try:
abi_type = grammar.parse(type_str)
except exceptions.ParseError:
return False
return abi_type.arrlist is not None | python | def has_arrlist(type_str):
"""
A predicate that matches a type string with an array dimension list.
"""
try:
abi_type = grammar.parse(type_str)
except exceptions.ParseError:
return False
return abi_type.arrlist is not None | [
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2,246 | ethereum/eth-abi | eth_abi/registry.py | is_base_tuple | def is_base_tuple(type_str):
"""
A predicate that matches a tuple type with no array dimension list.
"""
try:
abi_type = grammar.parse(type_str)
except exceptions.ParseError:
return False
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"""
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return False
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2,247 | ethereum/eth-abi | eth_abi/registry.py | ABIRegistry.register | def register(self, lookup: Lookup, encoder: Encoder, decoder: Decoder, label: str=None) -> None:
"""
Registers the given ``encoder`` and ``decoder`` under the given
``lookup``. A unique string label may be optionally provided that can
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:param lookup: A type string or type string matcher function
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:param label: An optional label that can be used to refer to this
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entry in the registry via the :any:`unregister` method and its
variants.
"""
self.register_encoder(lookup, encoder, label=label)
self.register_decoder(lookup, decoder, label=label) | python | def register(self, lookup: Lookup, encoder: Encoder, decoder: Decoder, label: str=None) -> None:
"""
Registers the given ``encoder`` and ``decoder`` under the given
``lookup``. A unique string label may be optionally provided that can
be used to refer to the registration by name.
:param lookup: A type string or type string matcher function
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self.register_encoder(lookup, encoder, label=label)
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2,248 | ethereum/eth-abi | eth_abi/registry.py | ABIRegistry.unregister | def unregister(self, label: str) -> None:
"""
Unregisters the entries in the encoder and decoder registries which
have the label ``label``.
"""
self.unregister_encoder(label)
self.unregister_decoder(label) | python | def unregister(self, label: str) -> None:
"""
Unregisters the entries in the encoder and decoder registries which
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self.unregister_encoder(label)
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2,249 | ethereum/eth-abi | eth_abi/registry.py | ABIRegistry.copy | def copy(self):
"""
Copies a registry such that new registrations can be made or existing
registrations can be unregistered without affecting any instance from
which a copy was obtained. This is useful if an existing registry
fulfills most of a user's needs but requires one or two modifications.
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changes made without affecting the original registry.
"""
cpy = type(self)()
cpy._encoders = copy.copy(self._encoders)
cpy._decoders = copy.copy(self._decoders)
return cpy | python | def copy(self):
"""
Copies a registry such that new registrations can be made or existing
registrations can be unregistered without affecting any instance from
which a copy was obtained. This is useful if an existing registry
fulfills most of a user's needs but requires one or two modifications.
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"""
cpy = type(self)()
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2,250 | ethereum/eth-abi | eth_abi/codec.py | ABIEncoder.encode_single | def encode_single(self, typ: TypeStr, arg: Any) -> bytes:
"""
Encodes the python value ``arg`` as a binary value of the ABI type
``typ``.
:param typ: The string representation of the ABI type that will be used
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etc.
:param arg: The python value to be encoded.
:returns: The binary representation of the python value ``arg`` as a
value of the ABI type ``typ``.
"""
encoder = self._registry.get_encoder(typ)
return encoder(arg) | python | def encode_single(self, typ: TypeStr, arg: Any) -> bytes:
"""
Encodes the python value ``arg`` as a binary value of the ABI type
``typ``.
:param typ: The string representation of the ABI type that will be used
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:param arg: The python value to be encoded.
:returns: The binary representation of the python value ``arg`` as a
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encoder = self._registry.get_encoder(typ)
return encoder(arg) | [
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2,251 | ethereum/eth-abi | eth_abi/codec.py | ABIEncoder.encode_abi | def encode_abi(self, types: Iterable[TypeStr], args: Iterable[Any]) -> bytes:
"""
Encodes the python values in ``args`` as a sequence of binary values of
the ABI types in ``types`` via the head-tail mechanism.
:param types: An iterable of string representations of the ABI types
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encoders = [
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encoder = TupleEncoder(encoders=encoders)
return encoder(args) | python | def encode_abi(self, types: Iterable[TypeStr], args: Iterable[Any]) -> bytes:
"""
Encodes the python values in ``args`` as a sequence of binary values of
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2,252 | ethereum/eth-abi | eth_abi/codec.py | ABIEncoder.is_encodable | def is_encodable(self, typ: TypeStr, arg: Any) -> bool:
"""
Determines if the python value ``arg`` is encodable as a value of the
ABI type ``typ``.
:param typ: A string representation for the ABI type against which the
python value ``arg`` will be checked e.g. ``'uint256'``,
``'bytes[]'``, ``'(int,int)'``, etc.
:param arg: The python value whose encodability should be checked.
:returns: ``True`` if ``arg`` is encodable as a value of the ABI type
``typ``. Otherwise, ``False``.
"""
encoder = self._registry.get_encoder(typ)
try:
encoder.validate_value(arg)
except EncodingError:
return False
except AttributeError:
try:
encoder(arg)
except EncodingError:
return False
return True | python | def is_encodable(self, typ: TypeStr, arg: Any) -> bool:
"""
Determines if the python value ``arg`` is encodable as a value of the
ABI type ``typ``.
:param typ: A string representation for the ABI type against which the
python value ``arg`` will be checked e.g. ``'uint256'``,
``'bytes[]'``, ``'(int,int)'``, etc.
:param arg: The python value whose encodability should be checked.
:returns: ``True`` if ``arg`` is encodable as a value of the ABI type
``typ``. Otherwise, ``False``.
"""
encoder = self._registry.get_encoder(typ)
try:
encoder.validate_value(arg)
except EncodingError:
return False
except AttributeError:
try:
encoder(arg)
except EncodingError:
return False
return True | [
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2,253 | ethereum/eth-abi | eth_abi/codec.py | ABIDecoder.decode_single | def decode_single(self, typ: TypeStr, data: Decodable) -> Any:
"""
Decodes the binary value ``data`` of the ABI type ``typ`` into its
equivalent python value.
:param typ: The string representation of the ABI type that will be used for
decoding e.g. ``'uint256'``, ``'bytes[]'``, ``'(int,int)'``, etc.
:param data: The binary value to be decoded.
:returns: The equivalent python value of the ABI value represented in
``data``.
"""
if not is_bytes(data):
raise TypeError("The `data` value must be of bytes type. Got {0}".format(type(data)))
decoder = self._registry.get_decoder(typ)
stream = ContextFramesBytesIO(data)
return decoder(stream) | python | def decode_single(self, typ: TypeStr, data: Decodable) -> Any:
"""
Decodes the binary value ``data`` of the ABI type ``typ`` into its
equivalent python value.
:param typ: The string representation of the ABI type that will be used for
decoding e.g. ``'uint256'``, ``'bytes[]'``, ``'(int,int)'``, etc.
:param data: The binary value to be decoded.
:returns: The equivalent python value of the ABI value represented in
``data``.
"""
if not is_bytes(data):
raise TypeError("The `data` value must be of bytes type. Got {0}".format(type(data)))
decoder = self._registry.get_decoder(typ)
stream = ContextFramesBytesIO(data)
return decoder(stream) | [
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2,254 | ethereum/eth-abi | eth_abi/codec.py | ABIDecoder.decode_abi | def decode_abi(self, types: Iterable[TypeStr], data: Decodable) -> Tuple[Any, ...]:
"""
Decodes the binary value ``data`` as a sequence of values of the ABI types
in ``types`` via the head-tail mechanism into a tuple of equivalent python
values.
:param types: An iterable of string representations of the ABI types that
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:param data: The binary value to be decoded.
:returns: A tuple of equivalent python values for the ABI values
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"""
if not is_bytes(data):
raise TypeError("The `data` value must be of bytes type. Got {0}".format(type(data)))
decoders = [
self._registry.get_decoder(type_str)
for type_str in types
]
decoder = TupleDecoder(decoders=decoders)
stream = ContextFramesBytesIO(data)
return decoder(stream) | python | def decode_abi(self, types: Iterable[TypeStr], data: Decodable) -> Tuple[Any, ...]:
"""
Decodes the binary value ``data`` as a sequence of values of the ABI types
in ``types`` via the head-tail mechanism into a tuple of equivalent python
values.
:param types: An iterable of string representations of the ABI types that
will be used for decoding e.g. ``('uint256', 'bytes[]', '(int,int)')``
:param data: The binary value to be decoded.
:returns: A tuple of equivalent python values for the ABI values
represented in ``data``.
"""
if not is_bytes(data):
raise TypeError("The `data` value must be of bytes type. Got {0}".format(type(data)))
decoders = [
self._registry.get_decoder(type_str)
for type_str in types
]
decoder = TupleDecoder(decoders=decoders)
stream = ContextFramesBytesIO(data)
return decoder(stream) | [
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2,255 | aiortc/aioice | aioice/turn.py | create_turn_endpoint | async def create_turn_endpoint(protocol_factory, server_addr, username, password,
lifetime=600, ssl=False, transport='udp'):
"""
Create datagram connection relayed over TURN.
"""
loop = asyncio.get_event_loop()
if transport == 'tcp':
_, inner_protocol = await loop.create_connection(
lambda: TurnClientTcpProtocol(server_addr,
username=username,
password=password,
lifetime=lifetime),
host=server_addr[0],
port=server_addr[1],
ssl=ssl)
else:
_, inner_protocol = await loop.create_datagram_endpoint(
lambda: TurnClientUdpProtocol(server_addr,
username=username,
password=password,
lifetime=lifetime),
remote_addr=server_addr)
protocol = protocol_factory()
transport = TurnTransport(protocol, inner_protocol)
await transport._connect()
return transport, protocol | python | async def create_turn_endpoint(protocol_factory, server_addr, username, password,
lifetime=600, ssl=False, transport='udp'):
"""
Create datagram connection relayed over TURN.
"""
loop = asyncio.get_event_loop()
if transport == 'tcp':
_, inner_protocol = await loop.create_connection(
lambda: TurnClientTcpProtocol(server_addr,
username=username,
password=password,
lifetime=lifetime),
host=server_addr[0],
port=server_addr[1],
ssl=ssl)
else:
_, inner_protocol = await loop.create_datagram_endpoint(
lambda: TurnClientUdpProtocol(server_addr,
username=username,
password=password,
lifetime=lifetime),
remote_addr=server_addr)
protocol = protocol_factory()
transport = TurnTransport(protocol, inner_protocol)
await transport._connect()
return transport, protocol | [
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2,256 | aiortc/aioice | aioice/turn.py | TurnClientMixin.connect | async def connect(self):
"""
Create a TURN allocation.
"""
request = stun.Message(message_method=stun.Method.ALLOCATE,
message_class=stun.Class.REQUEST)
request.attributes['LIFETIME'] = self.lifetime
request.attributes['REQUESTED-TRANSPORT'] = UDP_TRANSPORT
try:
response, _ = await self.request(request)
except exceptions.TransactionFailed as e:
response = e.response
if response.attributes['ERROR-CODE'][0] == 401:
# update long-term credentials
self.nonce = response.attributes['NONCE']
self.realm = response.attributes['REALM']
self.integrity_key = make_integrity_key(self.username, self.realm, self.password)
# retry request with authentication
request.transaction_id = random_transaction_id()
response, _ = await self.request(request)
self.relayed_address = response.attributes['XOR-RELAYED-ADDRESS']
logger.info('TURN allocation created %s', self.relayed_address)
# periodically refresh allocation
self.refresh_handle = asyncio.ensure_future(self.refresh())
return self.relayed_address | python | async def connect(self):
"""
Create a TURN allocation.
"""
request = stun.Message(message_method=stun.Method.ALLOCATE,
message_class=stun.Class.REQUEST)
request.attributes['LIFETIME'] = self.lifetime
request.attributes['REQUESTED-TRANSPORT'] = UDP_TRANSPORT
try:
response, _ = await self.request(request)
except exceptions.TransactionFailed as e:
response = e.response
if response.attributes['ERROR-CODE'][0] == 401:
# update long-term credentials
self.nonce = response.attributes['NONCE']
self.realm = response.attributes['REALM']
self.integrity_key = make_integrity_key(self.username, self.realm, self.password)
# retry request with authentication
request.transaction_id = random_transaction_id()
response, _ = await self.request(request)
self.relayed_address = response.attributes['XOR-RELAYED-ADDRESS']
logger.info('TURN allocation created %s', self.relayed_address)
# periodically refresh allocation
self.refresh_handle = asyncio.ensure_future(self.refresh())
return self.relayed_address | [
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2,257 | aiortc/aioice | aioice/turn.py | TurnClientMixin.delete | async def delete(self):
"""
Delete the TURN allocation.
"""
if self.refresh_handle:
self.refresh_handle.cancel()
self.refresh_handle = None
request = stun.Message(message_method=stun.Method.REFRESH,
message_class=stun.Class.REQUEST)
request.attributes['LIFETIME'] = 0
await self.request(request)
logger.info('TURN allocation deleted %s', self.relayed_address)
if self.receiver:
self.receiver.connection_lost(None) | python | async def delete(self):
"""
Delete the TURN allocation.
"""
if self.refresh_handle:
self.refresh_handle.cancel()
self.refresh_handle = None
request = stun.Message(message_method=stun.Method.REFRESH,
message_class=stun.Class.REQUEST)
request.attributes['LIFETIME'] = 0
await self.request(request)
logger.info('TURN allocation deleted %s', self.relayed_address)
if self.receiver:
self.receiver.connection_lost(None) | [
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2,258 | aiortc/aioice | aioice/turn.py | TurnClientMixin.refresh | async def refresh(self):
"""
Periodically refresh the TURN allocation.
"""
while True:
await asyncio.sleep(5/6 * self.lifetime)
request = stun.Message(message_method=stun.Method.REFRESH,
message_class=stun.Class.REQUEST)
request.attributes['LIFETIME'] = self.lifetime
await self.request(request)
logger.info('TURN allocation refreshed %s', self.relayed_address) | python | async def refresh(self):
"""
Periodically refresh the TURN allocation.
"""
while True:
await asyncio.sleep(5/6 * self.lifetime)
request = stun.Message(message_method=stun.Method.REFRESH,
message_class=stun.Class.REQUEST)
request.attributes['LIFETIME'] = self.lifetime
await self.request(request)
logger.info('TURN allocation refreshed %s', self.relayed_address) | [
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2,259 | aiortc/aioice | aioice/turn.py | TurnClientMixin.send_data | async def send_data(self, data, addr):
"""
Send data to a remote host via the TURN server.
"""
channel = self.peer_to_channel.get(addr)
if channel is None:
channel = self.channel_number
self.channel_number += 1
self.channel_to_peer[channel] = addr
self.peer_to_channel[addr] = channel
# bind channel
await self.channel_bind(channel, addr)
header = struct.pack('!HH', channel, len(data))
self._send(header + data) | python | async def send_data(self, data, addr):
"""
Send data to a remote host via the TURN server.
"""
channel = self.peer_to_channel.get(addr)
if channel is None:
channel = self.channel_number
self.channel_number += 1
self.channel_to_peer[channel] = addr
self.peer_to_channel[addr] = channel
# bind channel
await self.channel_bind(channel, addr)
header = struct.pack('!HH', channel, len(data))
self._send(header + data) | [
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2,260 | aiortc/aioice | aioice/turn.py | TurnClientMixin.send_stun | def send_stun(self, message, addr):
"""
Send a STUN message to the TURN server.
"""
logger.debug('%s > %s %s', self, addr, message)
self._send(bytes(message)) | python | def send_stun(self, message, addr):
"""
Send a STUN message to the TURN server.
"""
logger.debug('%s > %s %s', self, addr, message)
self._send(bytes(message)) | [
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2,261 | aiortc/aioice | aioice/turn.py | TurnTransport.get_extra_info | def get_extra_info(self, name, default=None):
"""
Return optional transport information.
- `'related_address'`: the related address
- `'sockname'`: the relayed address
"""
if name == 'related_address':
return self.__inner_protocol.transport.get_extra_info('sockname')
elif name == 'sockname':
return self.__relayed_address
return default | python | def get_extra_info(self, name, default=None):
"""
Return optional transport information.
- `'related_address'`: the related address
- `'sockname'`: the relayed address
"""
if name == 'related_address':
return self.__inner_protocol.transport.get_extra_info('sockname')
elif name == 'sockname':
return self.__relayed_address
return default | [
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2,262 | aiortc/aioice | aioice/turn.py | TurnTransport.sendto | def sendto(self, data, addr):
"""
Sends the `data` bytes to the remote peer given `addr`.
This will bind a TURN channel as necessary.
"""
asyncio.ensure_future(self.__inner_protocol.send_data(data, addr)) | python | def sendto(self, data, addr):
"""
Sends the `data` bytes to the remote peer given `addr`.
This will bind a TURN channel as necessary.
"""
asyncio.ensure_future(self.__inner_protocol.send_data(data, addr)) | [
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2,263 | aiortc/aioice | aioice/candidate.py | candidate_foundation | def candidate_foundation(candidate_type, candidate_transport, base_address):
"""
See RFC 5245 - 4.1.1.3. Computing Foundations
"""
key = '%s|%s|%s' % (candidate_type, candidate_transport, base_address)
return hashlib.md5(key.encode('ascii')).hexdigest() | python | def candidate_foundation(candidate_type, candidate_transport, base_address):
"""
See RFC 5245 - 4.1.1.3. Computing Foundations
"""
key = '%s|%s|%s' % (candidate_type, candidate_transport, base_address)
return hashlib.md5(key.encode('ascii')).hexdigest() | [
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2,264 | aiortc/aioice | aioice/candidate.py | candidate_priority | def candidate_priority(candidate_component, candidate_type, local_pref=65535):
"""
See RFC 5245 - 4.1.2.1. Recommended Formula
"""
if candidate_type == 'host':
type_pref = 126
elif candidate_type == 'prflx':
type_pref = 110
elif candidate_type == 'srflx':
type_pref = 100
else:
type_pref = 0
return (1 << 24) * type_pref + \
(1 << 8) * local_pref + \
(256 - candidate_component) | python | def candidate_priority(candidate_component, candidate_type, local_pref=65535):
"""
See RFC 5245 - 4.1.2.1. Recommended Formula
"""
if candidate_type == 'host':
type_pref = 126
elif candidate_type == 'prflx':
type_pref = 110
elif candidate_type == 'srflx':
type_pref = 100
else:
type_pref = 0
return (1 << 24) * type_pref + \
(1 << 8) * local_pref + \
(256 - candidate_component) | [
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2,265 | aiortc/aioice | aioice/candidate.py | Candidate.to_sdp | def to_sdp(self):
"""
Return a string representation suitable for SDP.
"""
sdp = '%s %d %s %d %s %d typ %s' % (
self.foundation,
self.component,
self.transport,
self.priority,
self.host,
self.port,
self.type)
if self.related_address is not None:
sdp += ' raddr %s' % self.related_address
if self.related_port is not None:
sdp += ' rport %s' % self.related_port
if self.tcptype is not None:
sdp += ' tcptype %s' % self.tcptype
if self.generation is not None:
sdp += ' generation %d' % self.generation
return sdp | python | def to_sdp(self):
"""
Return a string representation suitable for SDP.
"""
sdp = '%s %d %s %d %s %d typ %s' % (
self.foundation,
self.component,
self.transport,
self.priority,
self.host,
self.port,
self.type)
if self.related_address is not None:
sdp += ' raddr %s' % self.related_address
if self.related_port is not None:
sdp += ' rport %s' % self.related_port
if self.tcptype is not None:
sdp += ' tcptype %s' % self.tcptype
if self.generation is not None:
sdp += ' generation %d' % self.generation
return sdp | [
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2,266 | aiortc/aioice | aioice/candidate.py | Candidate.can_pair_with | def can_pair_with(self, other):
"""
A local candidate is paired with a remote candidate if and only if
the two candidates have the same component ID and have the same IP
address version.
"""
a = ipaddress.ip_address(self.host)
b = ipaddress.ip_address(other.host)
return (
self.component == other.component and
self.transport.lower() == other.transport.lower() and
a.version == b.version
) | python | def can_pair_with(self, other):
"""
A local candidate is paired with a remote candidate if and only if
the two candidates have the same component ID and have the same IP
address version.
"""
a = ipaddress.ip_address(self.host)
b = ipaddress.ip_address(other.host)
return (
self.component == other.component and
self.transport.lower() == other.transport.lower() and
a.version == b.version
) | [
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2,267 | aiortc/aioice | aioice/ice.py | candidate_pair_priority | def candidate_pair_priority(local, remote, ice_controlling):
"""
See RFC 5245 - 5.7.2. Computing Pair Priority and Ordering Pairs
"""
G = ice_controlling and local.priority or remote.priority
D = ice_controlling and remote.priority or local.priority
return (1 << 32) * min(G, D) + 2 * max(G, D) + (G > D and 1 or 0) | python | def candidate_pair_priority(local, remote, ice_controlling):
"""
See RFC 5245 - 5.7.2. Computing Pair Priority and Ordering Pairs
"""
G = ice_controlling and local.priority or remote.priority
D = ice_controlling and remote.priority or local.priority
return (1 << 32) * min(G, D) + 2 * max(G, D) + (G > D and 1 or 0) | [
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2,268 | aiortc/aioice | aioice/ice.py | get_host_addresses | def get_host_addresses(use_ipv4, use_ipv6):
"""
Get local IP addresses.
"""
addresses = []
for interface in netifaces.interfaces():
ifaddresses = netifaces.ifaddresses(interface)
for address in ifaddresses.get(socket.AF_INET, []):
if use_ipv4 and address['addr'] != '127.0.0.1':
addresses.append(address['addr'])
for address in ifaddresses.get(socket.AF_INET6, []):
if use_ipv6 and address['addr'] != '::1' and '%' not in address['addr']:
addresses.append(address['addr'])
return addresses | python | def get_host_addresses(use_ipv4, use_ipv6):
"""
Get local IP addresses.
"""
addresses = []
for interface in netifaces.interfaces():
ifaddresses = netifaces.ifaddresses(interface)
for address in ifaddresses.get(socket.AF_INET, []):
if use_ipv4 and address['addr'] != '127.0.0.1':
addresses.append(address['addr'])
for address in ifaddresses.get(socket.AF_INET6, []):
if use_ipv6 and address['addr'] != '::1' and '%' not in address['addr']:
addresses.append(address['addr'])
return addresses | [
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2,269 | aiortc/aioice | aioice/ice.py | server_reflexive_candidate | async def server_reflexive_candidate(protocol, stun_server):
"""
Query STUN server to obtain a server-reflexive candidate.
"""
# lookup address
loop = asyncio.get_event_loop()
stun_server = (
await loop.run_in_executor(None, socket.gethostbyname, stun_server[0]),
stun_server[1])
# perform STUN query
request = stun.Message(message_method=stun.Method.BINDING,
message_class=stun.Class.REQUEST)
response, _ = await protocol.request(request, stun_server)
local_candidate = protocol.local_candidate
return Candidate(
foundation=candidate_foundation('srflx', 'udp', local_candidate.host),
component=local_candidate.component,
transport=local_candidate.transport,
priority=candidate_priority(local_candidate.component, 'srflx'),
host=response.attributes['XOR-MAPPED-ADDRESS'][0],
port=response.attributes['XOR-MAPPED-ADDRESS'][1],
type='srflx',
related_address=local_candidate.host,
related_port=local_candidate.port) | python | async def server_reflexive_candidate(protocol, stun_server):
"""
Query STUN server to obtain a server-reflexive candidate.
"""
# lookup address
loop = asyncio.get_event_loop()
stun_server = (
await loop.run_in_executor(None, socket.gethostbyname, stun_server[0]),
stun_server[1])
# perform STUN query
request = stun.Message(message_method=stun.Method.BINDING,
message_class=stun.Class.REQUEST)
response, _ = await protocol.request(request, stun_server)
local_candidate = protocol.local_candidate
return Candidate(
foundation=candidate_foundation('srflx', 'udp', local_candidate.host),
component=local_candidate.component,
transport=local_candidate.transport,
priority=candidate_priority(local_candidate.component, 'srflx'),
host=response.attributes['XOR-MAPPED-ADDRESS'][0],
port=response.attributes['XOR-MAPPED-ADDRESS'][1],
type='srflx',
related_address=local_candidate.host,
related_port=local_candidate.port) | [
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2,270 | aiortc/aioice | aioice/ice.py | sort_candidate_pairs | def sort_candidate_pairs(pairs, ice_controlling):
"""
Sort a list of candidate pairs.
"""
def pair_priority(pair):
return -candidate_pair_priority(pair.local_candidate,
pair.remote_candidate,
ice_controlling)
pairs.sort(key=pair_priority) | python | def sort_candidate_pairs(pairs, ice_controlling):
"""
Sort a list of candidate pairs.
"""
def pair_priority(pair):
return -candidate_pair_priority(pair.local_candidate,
pair.remote_candidate,
ice_controlling)
pairs.sort(key=pair_priority) | [
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2,271 | aiortc/aioice | aioice/ice.py | StunProtocol.send_stun | def send_stun(self, message, addr):
"""
Send a STUN message.
"""
self.__log_debug('> %s %s', addr, message)
self.transport.sendto(bytes(message), addr) | python | def send_stun(self, message, addr):
"""
Send a STUN message.
"""
self.__log_debug('> %s %s', addr, message)
self.transport.sendto(bytes(message), addr) | [
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2,272 | aiortc/aioice | aioice/ice.py | Connection.add_remote_candidate | def add_remote_candidate(self, remote_candidate):
"""
Add a remote candidate or signal end-of-candidates.
To signal end-of-candidates, pass `None`.
"""
if self._remote_candidates_end:
raise ValueError('Cannot add remote candidate after end-of-candidates.')
if remote_candidate is None:
self._prune_components()
self._remote_candidates_end = True
return
self._remote_candidates.append(remote_candidate)
for protocol in self._protocols:
if (protocol.local_candidate.can_pair_with(remote_candidate) and
not self._find_pair(protocol, remote_candidate)):
pair = CandidatePair(protocol, remote_candidate)
self._check_list.append(pair)
self.sort_check_list() | python | def add_remote_candidate(self, remote_candidate):
"""
Add a remote candidate or signal end-of-candidates.
To signal end-of-candidates, pass `None`.
"""
if self._remote_candidates_end:
raise ValueError('Cannot add remote candidate after end-of-candidates.')
if remote_candidate is None:
self._prune_components()
self._remote_candidates_end = True
return
self._remote_candidates.append(remote_candidate)
for protocol in self._protocols:
if (protocol.local_candidate.can_pair_with(remote_candidate) and
not self._find_pair(protocol, remote_candidate)):
pair = CandidatePair(protocol, remote_candidate)
self._check_list.append(pair)
self.sort_check_list() | [
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2,273 | aiortc/aioice | aioice/ice.py | Connection.gather_candidates | async def gather_candidates(self):
"""
Gather local candidates.
You **must** call this coroutine before calling :meth:`connect`.
"""
if not self._local_candidates_start:
self._local_candidates_start = True
addresses = get_host_addresses(use_ipv4=self._use_ipv4, use_ipv6=self._use_ipv6)
for component in self._components:
self._local_candidates += await self.get_component_candidates(
component=component,
addresses=addresses)
self._local_candidates_end = True | python | async def gather_candidates(self):
"""
Gather local candidates.
You **must** call this coroutine before calling :meth:`connect`.
"""
if not self._local_candidates_start:
self._local_candidates_start = True
addresses = get_host_addresses(use_ipv4=self._use_ipv4, use_ipv6=self._use_ipv6)
for component in self._components:
self._local_candidates += await self.get_component_candidates(
component=component,
addresses=addresses)
self._local_candidates_end = True | [
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2,274 | aiortc/aioice | aioice/ice.py | Connection.get_default_candidate | def get_default_candidate(self, component):
"""
Gets the default local candidate for the specified component.
"""
for candidate in sorted(self._local_candidates, key=lambda x: x.priority):
if candidate.component == component:
return candidate | python | def get_default_candidate(self, component):
"""
Gets the default local candidate for the specified component.
"""
for candidate in sorted(self._local_candidates, key=lambda x: x.priority):
if candidate.component == component:
return candidate | [
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2,275 | aiortc/aioice | aioice/ice.py | Connection.connect | async def connect(self):
"""
Perform ICE handshake.
This coroutine returns if a candidate pair was successfuly nominated
and raises an exception otherwise.
"""
if not self._local_candidates_end:
raise ConnectionError('Local candidates gathering was not performed')
if (self.remote_username is None or
self.remote_password is None):
raise ConnectionError('Remote username or password is missing')
# 5.7.1. Forming Candidate Pairs
for remote_candidate in self._remote_candidates:
for protocol in self._protocols:
if (protocol.local_candidate.can_pair_with(remote_candidate) and
not self._find_pair(protocol, remote_candidate)):
pair = CandidatePair(protocol, remote_candidate)
self._check_list.append(pair)
self.sort_check_list()
self._unfreeze_initial()
# handle early checks
for check in self._early_checks:
self.check_incoming(*check)
self._early_checks = []
# perform checks
while True:
if not self.check_periodic():
break
await asyncio.sleep(0.02)
# wait for completion
if self._check_list:
res = await self._check_list_state.get()
else:
res = ICE_FAILED
# cancel remaining checks
for check in self._check_list:
if check.handle:
check.handle.cancel()
if res != ICE_COMPLETED:
raise ConnectionError('ICE negotiation failed')
# start consent freshness tests
self._query_consent_handle = asyncio.ensure_future(self.query_consent()) | python | async def connect(self):
"""
Perform ICE handshake.
This coroutine returns if a candidate pair was successfuly nominated
and raises an exception otherwise.
"""
if not self._local_candidates_end:
raise ConnectionError('Local candidates gathering was not performed')
if (self.remote_username is None or
self.remote_password is None):
raise ConnectionError('Remote username or password is missing')
# 5.7.1. Forming Candidate Pairs
for remote_candidate in self._remote_candidates:
for protocol in self._protocols:
if (protocol.local_candidate.can_pair_with(remote_candidate) and
not self._find_pair(protocol, remote_candidate)):
pair = CandidatePair(protocol, remote_candidate)
self._check_list.append(pair)
self.sort_check_list()
self._unfreeze_initial()
# handle early checks
for check in self._early_checks:
self.check_incoming(*check)
self._early_checks = []
# perform checks
while True:
if not self.check_periodic():
break
await asyncio.sleep(0.02)
# wait for completion
if self._check_list:
res = await self._check_list_state.get()
else:
res = ICE_FAILED
# cancel remaining checks
for check in self._check_list:
if check.handle:
check.handle.cancel()
if res != ICE_COMPLETED:
raise ConnectionError('ICE negotiation failed')
# start consent freshness tests
self._query_consent_handle = asyncio.ensure_future(self.query_consent()) | [
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2,276 | aiortc/aioice | aioice/ice.py | Connection.recvfrom | async def recvfrom(self):
"""
Receive the next datagram.
The return value is a `(bytes, component)` tuple where `bytes` is a
bytes object representing the data received and `component` is the
component on which the data was received.
If the connection is not established, a `ConnectionError` is raised.
"""
if not len(self._nominated):
raise ConnectionError('Cannot receive data, not connected')
result = await self._queue.get()
if result[0] is None:
raise ConnectionError('Connection lost while receiving data')
return result | python | async def recvfrom(self):
"""
Receive the next datagram.
The return value is a `(bytes, component)` tuple where `bytes` is a
bytes object representing the data received and `component` is the
component on which the data was received.
If the connection is not established, a `ConnectionError` is raised.
"""
if not len(self._nominated):
raise ConnectionError('Cannot receive data, not connected')
result = await self._queue.get()
if result[0] is None:
raise ConnectionError('Connection lost while receiving data')
return result | [
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2,277 | aiortc/aioice | aioice/ice.py | Connection.sendto | async def sendto(self, data, component):
"""
Send a datagram on the specified component.
If the connection is not established, a `ConnectionError` is raised.
"""
active_pair = self._nominated.get(component)
if active_pair:
await active_pair.protocol.send_data(data, active_pair.remote_addr)
else:
raise ConnectionError('Cannot send data, not connected') | python | async def sendto(self, data, component):
"""
Send a datagram on the specified component.
If the connection is not established, a `ConnectionError` is raised.
"""
active_pair = self._nominated.get(component)
if active_pair:
await active_pair.protocol.send_data(data, active_pair.remote_addr)
else:
raise ConnectionError('Cannot send data, not connected') | [
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If the connection is not established, a `ConnectionError` is raised. | [
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2,278 | aiortc/aioice | aioice/ice.py | Connection.set_selected_pair | def set_selected_pair(self, component, local_foundation, remote_foundation):
"""
Force the selected candidate pair.
If the remote party does not support ICE, you should using this
instead of calling :meth:`connect`.
"""
# find local candidate
protocol = None
for p in self._protocols:
if (p.local_candidate.component == component and
p.local_candidate.foundation == local_foundation):
protocol = p
break
# find remote candidate
remote_candidate = None
for c in self._remote_candidates:
if c.component == component and c.foundation == remote_foundation:
remote_candidate = c
assert (protocol and remote_candidate)
self._nominated[component] = CandidatePair(protocol, remote_candidate) | python | def set_selected_pair(self, component, local_foundation, remote_foundation):
"""
Force the selected candidate pair.
If the remote party does not support ICE, you should using this
instead of calling :meth:`connect`.
"""
# find local candidate
protocol = None
for p in self._protocols:
if (p.local_candidate.component == component and
p.local_candidate.foundation == local_foundation):
protocol = p
break
# find remote candidate
remote_candidate = None
for c in self._remote_candidates:
if c.component == component and c.foundation == remote_foundation:
remote_candidate = c
assert (protocol and remote_candidate)
self._nominated[component] = CandidatePair(protocol, remote_candidate) | [
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2,279 | aiortc/aioice | aioice/ice.py | Connection.check_incoming | def check_incoming(self, message, addr, protocol):
"""
Handle a succesful incoming check.
"""
component = protocol.local_candidate.component
# find remote candidate
remote_candidate = None
for c in self._remote_candidates:
if c.host == addr[0] and c.port == addr[1]:
remote_candidate = c
assert remote_candidate.component == component
break
if remote_candidate is None:
# 7.2.1.3. Learning Peer Reflexive Candidates
remote_candidate = Candidate(
foundation=random_string(10),
component=component,
transport='udp',
priority=message.attributes['PRIORITY'],
host=addr[0],
port=addr[1],
type='prflx')
self._remote_candidates.append(remote_candidate)
self.__log_info('Discovered peer reflexive candidate %s', remote_candidate)
# find pair
pair = self._find_pair(protocol, remote_candidate)
if pair is None:
pair = CandidatePair(protocol, remote_candidate)
pair.state = CandidatePair.State.WAITING
self._check_list.append(pair)
self.sort_check_list()
# triggered check
if pair.state in [CandidatePair.State.WAITING, CandidatePair.State.FAILED]:
pair.handle = asyncio.ensure_future(self.check_start(pair))
# 7.2.1.5. Updating the Nominated Flag
if 'USE-CANDIDATE' in message.attributes and not self.ice_controlling:
pair.remote_nominated = True
if pair.state == CandidatePair.State.SUCCEEDED:
pair.nominated = True
self.check_complete(pair) | python | def check_incoming(self, message, addr, protocol):
"""
Handle a succesful incoming check.
"""
component = protocol.local_candidate.component
# find remote candidate
remote_candidate = None
for c in self._remote_candidates:
if c.host == addr[0] and c.port == addr[1]:
remote_candidate = c
assert remote_candidate.component == component
break
if remote_candidate is None:
# 7.2.1.3. Learning Peer Reflexive Candidates
remote_candidate = Candidate(
foundation=random_string(10),
component=component,
transport='udp',
priority=message.attributes['PRIORITY'],
host=addr[0],
port=addr[1],
type='prflx')
self._remote_candidates.append(remote_candidate)
self.__log_info('Discovered peer reflexive candidate %s', remote_candidate)
# find pair
pair = self._find_pair(protocol, remote_candidate)
if pair is None:
pair = CandidatePair(protocol, remote_candidate)
pair.state = CandidatePair.State.WAITING
self._check_list.append(pair)
self.sort_check_list()
# triggered check
if pair.state in [CandidatePair.State.WAITING, CandidatePair.State.FAILED]:
pair.handle = asyncio.ensure_future(self.check_start(pair))
# 7.2.1.5. Updating the Nominated Flag
if 'USE-CANDIDATE' in message.attributes and not self.ice_controlling:
pair.remote_nominated = True
if pair.state == CandidatePair.State.SUCCEEDED:
pair.nominated = True
self.check_complete(pair) | [
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2,280 | aiortc/aioice | aioice/ice.py | Connection.check_start | async def check_start(self, pair):
"""
Starts a check.
"""
self.check_state(pair, CandidatePair.State.IN_PROGRESS)
request = self.build_request(pair)
try:
response, addr = await pair.protocol.request(
request, pair.remote_addr,
integrity_key=self.remote_password.encode('utf8'))
except exceptions.TransactionError as exc:
# 7.1.3.1. Failure Cases
if exc.response and exc.response.attributes.get('ERROR-CODE', (None, None))[0] == 487:
if 'ICE-CONTROLLING' in request.attributes:
self.switch_role(ice_controlling=False)
elif 'ICE-CONTROLLED' in request.attributes:
self.switch_role(ice_controlling=True)
return await self.check_start(pair)
else:
self.check_state(pair, CandidatePair.State.FAILED)
self.check_complete(pair)
return
# check remote address matches
if addr != pair.remote_addr:
self.__log_info('Check %s failed : source address mismatch', pair)
self.check_state(pair, CandidatePair.State.FAILED)
self.check_complete(pair)
return
# success
self.check_state(pair, CandidatePair.State.SUCCEEDED)
if self.ice_controlling or pair.remote_nominated:
pair.nominated = True
self.check_complete(pair) | python | async def check_start(self, pair):
"""
Starts a check.
"""
self.check_state(pair, CandidatePair.State.IN_PROGRESS)
request = self.build_request(pair)
try:
response, addr = await pair.protocol.request(
request, pair.remote_addr,
integrity_key=self.remote_password.encode('utf8'))
except exceptions.TransactionError as exc:
# 7.1.3.1. Failure Cases
if exc.response and exc.response.attributes.get('ERROR-CODE', (None, None))[0] == 487:
if 'ICE-CONTROLLING' in request.attributes:
self.switch_role(ice_controlling=False)
elif 'ICE-CONTROLLED' in request.attributes:
self.switch_role(ice_controlling=True)
return await self.check_start(pair)
else:
self.check_state(pair, CandidatePair.State.FAILED)
self.check_complete(pair)
return
# check remote address matches
if addr != pair.remote_addr:
self.__log_info('Check %s failed : source address mismatch', pair)
self.check_state(pair, CandidatePair.State.FAILED)
self.check_complete(pair)
return
# success
self.check_state(pair, CandidatePair.State.SUCCEEDED)
if self.ice_controlling or pair.remote_nominated:
pair.nominated = True
self.check_complete(pair) | [
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2,281 | aiortc/aioice | aioice/ice.py | Connection.check_state | def check_state(self, pair, state):
"""
Updates the state of a check.
"""
self.__log_info('Check %s %s -> %s', pair, pair.state, state)
pair.state = state | python | def check_state(self, pair, state):
"""
Updates the state of a check.
"""
self.__log_info('Check %s %s -> %s', pair, pair.state, state)
pair.state = state | [
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2,282 | aiortc/aioice | aioice/ice.py | Connection._find_pair | def _find_pair(self, protocol, remote_candidate):
"""
Find a candidate pair in the check list.
"""
for pair in self._check_list:
if (pair.protocol == protocol and pair.remote_candidate == remote_candidate):
return pair
return None | python | def _find_pair(self, protocol, remote_candidate):
"""
Find a candidate pair in the check list.
"""
for pair in self._check_list:
if (pair.protocol == protocol and pair.remote_candidate == remote_candidate):
return pair
return None | [
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2,283 | aiortc/aioice | aioice/ice.py | Connection._prune_components | def _prune_components(self):
"""
Remove components for which the remote party did not provide any candidates.
This can only be determined after end-of-candidates.
"""
seen_components = set(map(lambda x: x.component, self._remote_candidates))
missing_components = self._components - seen_components
if missing_components:
self.__log_info('Components %s have no candidate pairs' % missing_components)
self._components = seen_components | python | def _prune_components(self):
"""
Remove components for which the remote party did not provide any candidates.
This can only be determined after end-of-candidates.
"""
seen_components = set(map(lambda x: x.component, self._remote_candidates))
missing_components = self._components - seen_components
if missing_components:
self.__log_info('Components %s have no candidate pairs' % missing_components)
self._components = seen_components | [
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2,284 | aiortc/aioice | aioice/stun.py | parse_message | def parse_message(data, integrity_key=None):
"""
Parses a STUN message.
If the ``integrity_key`` parameter is given, the message's HMAC will be verified.
"""
if len(data) < HEADER_LENGTH:
raise ValueError('STUN message length is less than 20 bytes')
message_type, length, cookie, transaction_id = unpack('!HHI12s', data[0:HEADER_LENGTH])
if len(data) != HEADER_LENGTH + length:
raise ValueError('STUN message length does not match')
attributes = OrderedDict()
pos = HEADER_LENGTH
while pos <= len(data) - 4:
attr_type, attr_len = unpack('!HH', data[pos:pos + 4])
v = data[pos + 4:pos + 4 + attr_len]
pad_len = 4 * ((attr_len + 3) // 4) - attr_len
if attr_type in ATTRIBUTES_BY_TYPE:
_, attr_name, attr_pack, attr_unpack = ATTRIBUTES_BY_TYPE[attr_type]
if attr_unpack == unpack_xor_address:
attributes[attr_name] = attr_unpack(v, transaction_id=transaction_id)
else:
attributes[attr_name] = attr_unpack(v)
if attr_name == 'FINGERPRINT':
if attributes[attr_name] != message_fingerprint(data[0:pos]):
raise ValueError('STUN message fingerprint does not match')
elif attr_name == 'MESSAGE-INTEGRITY':
if (integrity_key is not None and
attributes[attr_name] != message_integrity(data[0:pos], integrity_key)):
raise ValueError('STUN message integrity does not match')
pos += 4 + attr_len + pad_len
return Message(
message_method=message_type & 0x3eef,
message_class=message_type & 0x0110,
transaction_id=transaction_id,
attributes=attributes) | python | def parse_message(data, integrity_key=None):
"""
Parses a STUN message.
If the ``integrity_key`` parameter is given, the message's HMAC will be verified.
"""
if len(data) < HEADER_LENGTH:
raise ValueError('STUN message length is less than 20 bytes')
message_type, length, cookie, transaction_id = unpack('!HHI12s', data[0:HEADER_LENGTH])
if len(data) != HEADER_LENGTH + length:
raise ValueError('STUN message length does not match')
attributes = OrderedDict()
pos = HEADER_LENGTH
while pos <= len(data) - 4:
attr_type, attr_len = unpack('!HH', data[pos:pos + 4])
v = data[pos + 4:pos + 4 + attr_len]
pad_len = 4 * ((attr_len + 3) // 4) - attr_len
if attr_type in ATTRIBUTES_BY_TYPE:
_, attr_name, attr_pack, attr_unpack = ATTRIBUTES_BY_TYPE[attr_type]
if attr_unpack == unpack_xor_address:
attributes[attr_name] = attr_unpack(v, transaction_id=transaction_id)
else:
attributes[attr_name] = attr_unpack(v)
if attr_name == 'FINGERPRINT':
if attributes[attr_name] != message_fingerprint(data[0:pos]):
raise ValueError('STUN message fingerprint does not match')
elif attr_name == 'MESSAGE-INTEGRITY':
if (integrity_key is not None and
attributes[attr_name] != message_integrity(data[0:pos], integrity_key)):
raise ValueError('STUN message integrity does not match')
pos += 4 + attr_len + pad_len
return Message(
message_method=message_type & 0x3eef,
message_class=message_type & 0x0110,
transaction_id=transaction_id,
attributes=attributes) | [
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2,285 | cole/aiosmtplib | src/aiosmtplib/protocol.py | SMTPProtocol.connection_made | def connection_made(self, transport: asyncio.BaseTransport) -> None:
"""
Modified ``connection_made`` that supports upgrading our transport in
place using STARTTLS.
We set the _transport directly on the StreamReader, rather than calling
set_transport (which will raise an AssertionError on upgrade).
"""
if self._stream_reader is None:
raise SMTPServerDisconnected("Client not connected")
self._stream_reader._transport = transport # type: ignore
self._over_ssl = transport.get_extra_info("sslcontext") is not None
self._stream_writer = asyncio.StreamWriter(
transport, self, self._stream_reader, self._loop
)
self._client_connected_cb( # type: ignore
self._stream_reader, self._stream_writer
) | python | def connection_made(self, transport: asyncio.BaseTransport) -> None:
"""
Modified ``connection_made`` that supports upgrading our transport in
place using STARTTLS.
We set the _transport directly on the StreamReader, rather than calling
set_transport (which will raise an AssertionError on upgrade).
"""
if self._stream_reader is None:
raise SMTPServerDisconnected("Client not connected")
self._stream_reader._transport = transport # type: ignore
self._over_ssl = transport.get_extra_info("sslcontext") is not None
self._stream_writer = asyncio.StreamWriter(
transport, self, self._stream_reader, self._loop
)
self._client_connected_cb( # type: ignore
self._stream_reader, self._stream_writer
) | [
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2,286 | cole/aiosmtplib | src/aiosmtplib/protocol.py | SMTPProtocol.upgrade_transport | def upgrade_transport(
self,
context: ssl.SSLContext,
server_hostname: str = None,
waiter: Awaitable = None,
) -> SSLProtocol:
"""
Upgrade our transport to TLS in place.
"""
if self._over_ssl:
raise RuntimeError("Already using TLS.")
if self._stream_reader is None or self._stream_writer is None:
raise SMTPServerDisconnected("Client not connected")
transport = self._stream_reader._transport # type: ignore
tls_protocol = SSLProtocol(
self._loop,
self,
context,
waiter,
server_side=False,
server_hostname=server_hostname,
)
app_transport = tls_protocol._app_transport
# Use set_protocol if we can
if hasattr(transport, "set_protocol"):
transport.set_protocol(tls_protocol)
else:
transport._protocol = tls_protocol
self._stream_reader._transport = app_transport # type: ignore
self._stream_writer._transport = app_transport # type: ignore
tls_protocol.connection_made(transport)
self._over_ssl = True # type: bool
return tls_protocol | python | def upgrade_transport(
self,
context: ssl.SSLContext,
server_hostname: str = None,
waiter: Awaitable = None,
) -> SSLProtocol:
"""
Upgrade our transport to TLS in place.
"""
if self._over_ssl:
raise RuntimeError("Already using TLS.")
if self._stream_reader is None or self._stream_writer is None:
raise SMTPServerDisconnected("Client not connected")
transport = self._stream_reader._transport # type: ignore
tls_protocol = SSLProtocol(
self._loop,
self,
context,
waiter,
server_side=False,
server_hostname=server_hostname,
)
app_transport = tls_protocol._app_transport
# Use set_protocol if we can
if hasattr(transport, "set_protocol"):
transport.set_protocol(tls_protocol)
else:
transport._protocol = tls_protocol
self._stream_reader._transport = app_transport # type: ignore
self._stream_writer._transport = app_transport # type: ignore
tls_protocol.connection_made(transport)
self._over_ssl = True # type: bool
return tls_protocol | [
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2,287 | cole/aiosmtplib | src/aiosmtplib/protocol.py | SMTPProtocol.read_response | async def read_response(self, timeout: NumType = None) -> SMTPResponse:
"""
Get a status reponse from the server.
Returns an SMTPResponse namedtuple consisting of:
- server response code (e.g. 250, or such, if all goes well)
- server response string corresponding to response code (multiline
responses are converted to a single, multiline string).
"""
if self._stream_reader is None:
raise SMTPServerDisconnected("Client not connected")
code = None
response_lines = []
while True:
async with self._io_lock:
line = await self._readline(timeout=timeout)
try:
code = int(line[:3])
except ValueError:
pass
message = line[4:].strip(b" \t\r\n").decode("utf-8", "surrogateescape")
response_lines.append(message)
if line[3:4] != b"-":
break
full_message = "\n".join(response_lines)
if code is None:
raise SMTPResponseException(
SMTPStatus.invalid_response.value,
"Malformed SMTP response: {}".format(full_message),
)
return SMTPResponse(code, full_message) | python | async def read_response(self, timeout: NumType = None) -> SMTPResponse:
"""
Get a status reponse from the server.
Returns an SMTPResponse namedtuple consisting of:
- server response code (e.g. 250, or such, if all goes well)
- server response string corresponding to response code (multiline
responses are converted to a single, multiline string).
"""
if self._stream_reader is None:
raise SMTPServerDisconnected("Client not connected")
code = None
response_lines = []
while True:
async with self._io_lock:
line = await self._readline(timeout=timeout)
try:
code = int(line[:3])
except ValueError:
pass
message = line[4:].strip(b" \t\r\n").decode("utf-8", "surrogateescape")
response_lines.append(message)
if line[3:4] != b"-":
break
full_message = "\n".join(response_lines)
if code is None:
raise SMTPResponseException(
SMTPStatus.invalid_response.value,
"Malformed SMTP response: {}".format(full_message),
)
return SMTPResponse(code, full_message) | [
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2,288 | cole/aiosmtplib | src/aiosmtplib/protocol.py | SMTPProtocol.write_and_drain | async def write_and_drain(self, data: bytes, timeout: NumType = None) -> None:
"""
Format a command and send it to the server.
"""
if self._stream_writer is None:
raise SMTPServerDisconnected("Client not connected")
self._stream_writer.write(data)
async with self._io_lock:
await self._drain_writer(timeout) | python | async def write_and_drain(self, data: bytes, timeout: NumType = None) -> None:
"""
Format a command and send it to the server.
"""
if self._stream_writer is None:
raise SMTPServerDisconnected("Client not connected")
self._stream_writer.write(data)
async with self._io_lock:
await self._drain_writer(timeout) | [
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2,289 | cole/aiosmtplib | src/aiosmtplib/protocol.py | SMTPProtocol.write_message_data | async def write_message_data(self, data: bytes, timeout: NumType = None) -> None:
"""
Encode and write email message data.
Automatically quotes lines beginning with a period per RFC821.
Lone \\\\r and \\\\n characters are converted to \\\\r\\\\n
characters.
"""
data = LINE_ENDINGS_REGEX.sub(b"\r\n", data)
data = PERIOD_REGEX.sub(b"..", data)
if not data.endswith(b"\r\n"):
data += b"\r\n"
data += b".\r\n"
await self.write_and_drain(data, timeout=timeout) | python | async def write_message_data(self, data: bytes, timeout: NumType = None) -> None:
"""
Encode and write email message data.
Automatically quotes lines beginning with a period per RFC821.
Lone \\\\r and \\\\n characters are converted to \\\\r\\\\n
characters.
"""
data = LINE_ENDINGS_REGEX.sub(b"\r\n", data)
data = PERIOD_REGEX.sub(b"..", data)
if not data.endswith(b"\r\n"):
data += b"\r\n"
data += b".\r\n"
await self.write_and_drain(data, timeout=timeout) | [
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2,290 | cole/aiosmtplib | src/aiosmtplib/protocol.py | SMTPProtocol.execute_command | async def execute_command(
self, *args: bytes, timeout: NumType = None
) -> SMTPResponse:
"""
Sends an SMTP command along with any args to the server, and returns
a response.
"""
command = b" ".join(args) + b"\r\n"
await self.write_and_drain(command, timeout=timeout)
response = await self.read_response(timeout=timeout)
return response | python | async def execute_command(
self, *args: bytes, timeout: NumType = None
) -> SMTPResponse:
"""
Sends an SMTP command along with any args to the server, and returns
a response.
"""
command = b" ".join(args) + b"\r\n"
await self.write_and_drain(command, timeout=timeout)
response = await self.read_response(timeout=timeout)
return response | [
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] | 0cd00e5059005371cbdfca995feff9183a16a51f | https://github.com/cole/aiosmtplib/blob/0cd00e5059005371cbdfca995feff9183a16a51f/src/aiosmtplib/protocol.py#L178-L190 |
2,291 | cole/aiosmtplib | src/aiosmtplib/esmtp.py | ESMTP.last_ehlo_response | def last_ehlo_response(self, response: SMTPResponse) -> None:
"""
When setting the last EHLO response, parse the message for supported
extensions and auth methods.
"""
extensions, auth_methods = parse_esmtp_extensions(response.message)
self._last_ehlo_response = response
self.esmtp_extensions = extensions
self.server_auth_methods = auth_methods
self.supports_esmtp = True | python | def last_ehlo_response(self, response: SMTPResponse) -> None:
"""
When setting the last EHLO response, parse the message for supported
extensions and auth methods.
"""
extensions, auth_methods = parse_esmtp_extensions(response.message)
self._last_ehlo_response = response
self.esmtp_extensions = extensions
self.server_auth_methods = auth_methods
self.supports_esmtp = True | [
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2,292 | cole/aiosmtplib | src/aiosmtplib/esmtp.py | ESMTP.helo | async def helo(
self, hostname: str = None, timeout: DefaultNumType = _default
) -> SMTPResponse:
"""
Send the SMTP HELO command.
Hostname to send for this command defaults to the FQDN of the local
host.
:raises SMTPHeloError: on unexpected server response code
"""
if hostname is None:
hostname = self.source_address
async with self._command_lock:
response = await self.execute_command(
b"HELO", hostname.encode("ascii"), timeout=timeout
)
self.last_helo_response = response
if response.code != SMTPStatus.completed:
raise SMTPHeloError(response.code, response.message)
return response | python | async def helo(
self, hostname: str = None, timeout: DefaultNumType = _default
) -> SMTPResponse:
"""
Send the SMTP HELO command.
Hostname to send for this command defaults to the FQDN of the local
host.
:raises SMTPHeloError: on unexpected server response code
"""
if hostname is None:
hostname = self.source_address
async with self._command_lock:
response = await self.execute_command(
b"HELO", hostname.encode("ascii"), timeout=timeout
)
self.last_helo_response = response
if response.code != SMTPStatus.completed:
raise SMTPHeloError(response.code, response.message)
return response | [
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2,293 | cole/aiosmtplib | src/aiosmtplib/esmtp.py | ESMTP.help | async def help(self, timeout: DefaultNumType = _default) -> str:
"""
Send the SMTP HELP command, which responds with help text.
:raises SMTPResponseException: on unexpected server response code
"""
await self._ehlo_or_helo_if_needed()
async with self._command_lock:
response = await self.execute_command(b"HELP", timeout=timeout)
success_codes = (
SMTPStatus.system_status_ok,
SMTPStatus.help_message,
SMTPStatus.completed,
)
if response.code not in success_codes:
raise SMTPResponseException(response.code, response.message)
return response.message | python | async def help(self, timeout: DefaultNumType = _default) -> str:
"""
Send the SMTP HELP command, which responds with help text.
:raises SMTPResponseException: on unexpected server response code
"""
await self._ehlo_or_helo_if_needed()
async with self._command_lock:
response = await self.execute_command(b"HELP", timeout=timeout)
success_codes = (
SMTPStatus.system_status_ok,
SMTPStatus.help_message,
SMTPStatus.completed,
)
if response.code not in success_codes:
raise SMTPResponseException(response.code, response.message)
return response.message | [
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2,294 | cole/aiosmtplib | src/aiosmtplib/esmtp.py | ESMTP.noop | async def noop(self, timeout: DefaultNumType = _default) -> SMTPResponse:
"""
Send an SMTP NOOP command, which does nothing.
:raises SMTPResponseException: on unexpected server response code
"""
await self._ehlo_or_helo_if_needed()
async with self._command_lock:
response = await self.execute_command(b"NOOP", timeout=timeout)
if response.code != SMTPStatus.completed:
raise SMTPResponseException(response.code, response.message)
return response | python | async def noop(self, timeout: DefaultNumType = _default) -> SMTPResponse:
"""
Send an SMTP NOOP command, which does nothing.
:raises SMTPResponseException: on unexpected server response code
"""
await self._ehlo_or_helo_if_needed()
async with self._command_lock:
response = await self.execute_command(b"NOOP", timeout=timeout)
if response.code != SMTPStatus.completed:
raise SMTPResponseException(response.code, response.message)
return response | [
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2,295 | cole/aiosmtplib | src/aiosmtplib/esmtp.py | ESMTP.vrfy | async def vrfy(
self, address: str, timeout: DefaultNumType = _default
) -> SMTPResponse:
"""
Send an SMTP VRFY command, which tests an address for validity.
Not many servers support this command.
:raises SMTPResponseException: on unexpected server response code
"""
await self._ehlo_or_helo_if_needed()
parsed_address = parse_address(address)
async with self._command_lock:
response = await self.execute_command(
b"VRFY", parsed_address.encode("ascii"), timeout=timeout
)
success_codes = (
SMTPStatus.completed,
SMTPStatus.will_forward,
SMTPStatus.cannot_vrfy,
)
if response.code not in success_codes:
raise SMTPResponseException(response.code, response.message)
return response | python | async def vrfy(
self, address: str, timeout: DefaultNumType = _default
) -> SMTPResponse:
"""
Send an SMTP VRFY command, which tests an address for validity.
Not many servers support this command.
:raises SMTPResponseException: on unexpected server response code
"""
await self._ehlo_or_helo_if_needed()
parsed_address = parse_address(address)
async with self._command_lock:
response = await self.execute_command(
b"VRFY", parsed_address.encode("ascii"), timeout=timeout
)
success_codes = (
SMTPStatus.completed,
SMTPStatus.will_forward,
SMTPStatus.cannot_vrfy,
)
if response.code not in success_codes:
raise SMTPResponseException(response.code, response.message)
return response | [
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2,296 | cole/aiosmtplib | src/aiosmtplib/esmtp.py | ESMTP.expn | async def expn(
self, address: str, timeout: DefaultNumType = _default
) -> SMTPResponse:
"""
Send an SMTP EXPN command, which expands a mailing list.
Not many servers support this command.
:raises SMTPResponseException: on unexpected server response code
"""
await self._ehlo_or_helo_if_needed()
parsed_address = parse_address(address)
async with self._command_lock:
response = await self.execute_command(
b"EXPN", parsed_address.encode("ascii"), timeout=timeout
)
if response.code != SMTPStatus.completed:
raise SMTPResponseException(response.code, response.message)
return response | python | async def expn(
self, address: str, timeout: DefaultNumType = _default
) -> SMTPResponse:
"""
Send an SMTP EXPN command, which expands a mailing list.
Not many servers support this command.
:raises SMTPResponseException: on unexpected server response code
"""
await self._ehlo_or_helo_if_needed()
parsed_address = parse_address(address)
async with self._command_lock:
response = await self.execute_command(
b"EXPN", parsed_address.encode("ascii"), timeout=timeout
)
if response.code != SMTPStatus.completed:
raise SMTPResponseException(response.code, response.message)
return response | [
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2,297 | cole/aiosmtplib | src/aiosmtplib/esmtp.py | ESMTP.quit | async def quit(self, timeout: DefaultNumType = _default) -> SMTPResponse:
"""
Send the SMTP QUIT command, which closes the connection.
Also closes the connection from our side after a response is received.
:raises SMTPResponseException: on unexpected server response code
"""
# Can't quit without HELO/EHLO
await self._ehlo_or_helo_if_needed()
async with self._command_lock:
response = await self.execute_command(b"QUIT", timeout=timeout)
if response.code != SMTPStatus.closing:
raise SMTPResponseException(response.code, response.message)
self.close()
return response | python | async def quit(self, timeout: DefaultNumType = _default) -> SMTPResponse:
"""
Send the SMTP QUIT command, which closes the connection.
Also closes the connection from our side after a response is received.
:raises SMTPResponseException: on unexpected server response code
"""
# Can't quit without HELO/EHLO
await self._ehlo_or_helo_if_needed()
async with self._command_lock:
response = await self.execute_command(b"QUIT", timeout=timeout)
if response.code != SMTPStatus.closing:
raise SMTPResponseException(response.code, response.message)
self.close()
return response | [
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2,298 | cole/aiosmtplib | src/aiosmtplib/esmtp.py | ESMTP.rcpt | async def rcpt(
self,
recipient: str,
options: Iterable[str] = None,
timeout: DefaultNumType = _default,
) -> SMTPResponse:
"""
Send an SMTP RCPT command, which specifies a single recipient for
the message. This command is sent once per recipient and must be
preceded by 'MAIL'.
:raises SMTPRecipientRefused: on unexpected server response code
"""
await self._ehlo_or_helo_if_needed()
if options is None:
options = []
options_bytes = [option.encode("ascii") for option in options]
to = b"TO:" + quote_address(recipient).encode("ascii")
async with self._command_lock:
response = await self.execute_command(
b"RCPT", to, *options_bytes, timeout=timeout
)
success_codes = (SMTPStatus.completed, SMTPStatus.will_forward)
if response.code not in success_codes:
raise SMTPRecipientRefused(response.code, response.message, recipient)
return response | python | async def rcpt(
self,
recipient: str,
options: Iterable[str] = None,
timeout: DefaultNumType = _default,
) -> SMTPResponse:
"""
Send an SMTP RCPT command, which specifies a single recipient for
the message. This command is sent once per recipient and must be
preceded by 'MAIL'.
:raises SMTPRecipientRefused: on unexpected server response code
"""
await self._ehlo_or_helo_if_needed()
if options is None:
options = []
options_bytes = [option.encode("ascii") for option in options]
to = b"TO:" + quote_address(recipient).encode("ascii")
async with self._command_lock:
response = await self.execute_command(
b"RCPT", to, *options_bytes, timeout=timeout
)
success_codes = (SMTPStatus.completed, SMTPStatus.will_forward)
if response.code not in success_codes:
raise SMTPRecipientRefused(response.code, response.message, recipient)
return response | [
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the message. This command is sent once per recipient and must be
preceded by 'MAIL'.
:raises SMTPRecipientRefused: on unexpected server response code | [
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2,299 | cole/aiosmtplib | src/aiosmtplib/esmtp.py | ESMTP.data | async def data(
self, message: Union[str, bytes], timeout: DefaultNumType = _default
) -> SMTPResponse:
"""
Send an SMTP DATA command, followed by the message given.
This method transfers the actual email content to the server.
:raises SMTPDataError: on unexpected server response code
:raises SMTPServerDisconnected: connection lost
"""
await self._ehlo_or_helo_if_needed()
# As data accesses protocol directly, some handling is required
self._raise_error_if_disconnected()
if timeout is _default:
timeout = self.timeout # type: ignore
if isinstance(message, str):
message = message.encode("ascii")
async with self._command_lock:
start_response = await self.execute_command(b"DATA", timeout=timeout)
if start_response.code != SMTPStatus.start_input:
raise SMTPDataError(start_response.code, start_response.message)
try:
await self.protocol.write_message_data( # type: ignore
message, timeout=timeout
)
response = await self.protocol.read_response( # type: ignore
timeout=timeout
)
except SMTPServerDisconnected as exc:
self.close()
raise exc
if response.code != SMTPStatus.completed:
raise SMTPDataError(response.code, response.message)
return response | python | async def data(
self, message: Union[str, bytes], timeout: DefaultNumType = _default
) -> SMTPResponse:
"""
Send an SMTP DATA command, followed by the message given.
This method transfers the actual email content to the server.
:raises SMTPDataError: on unexpected server response code
:raises SMTPServerDisconnected: connection lost
"""
await self._ehlo_or_helo_if_needed()
# As data accesses protocol directly, some handling is required
self._raise_error_if_disconnected()
if timeout is _default:
timeout = self.timeout # type: ignore
if isinstance(message, str):
message = message.encode("ascii")
async with self._command_lock:
start_response = await self.execute_command(b"DATA", timeout=timeout)
if start_response.code != SMTPStatus.start_input:
raise SMTPDataError(start_response.code, start_response.message)
try:
await self.protocol.write_message_data( # type: ignore
message, timeout=timeout
)
response = await self.protocol.read_response( # type: ignore
timeout=timeout
)
except SMTPServerDisconnected as exc:
self.close()
raise exc
if response.code != SMTPStatus.completed:
raise SMTPDataError(response.code, response.message)
return response | [
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This method transfers the actual email content to the server.
:raises SMTPDataError: on unexpected server response code
:raises SMTPServerDisconnected: connection lost | [
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Subsets and Splits