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calmjs/calmjs | src/calmjs/ui.py | prompt_overwrite_json | def prompt_overwrite_json(original, new, target_path, dumps=json_dumps):
"""
Prompt end user with a diff of original and new json that may
overwrite the file at the target_path. This function only displays
a confirmation prompt and it is up to the caller to implement the
actual functionality. Optionally, a custom json.dumps method can
also be passed in for output generation.
"""
# generate compacted ndiff output.
diff = '\n'.join(l for l in (
line.rstrip() for line in difflib.ndiff(
json_dumps(original).splitlines(),
json_dumps(new).splitlines(),
))
if l[:1] in '?+-' or l[-1:] in '{}' or l[-2:] == '},')
basename_target = basename(target_path)
return prompt(
"Generated '%(basename_target)s' differs with '%(target_path)s'.\n\n"
"The following is a compacted list of changes required:\n"
"%(diff)s\n\n"
"Overwrite '%(target_path)s'?" % locals(),
choices=(
('Yes', True),
('No', False),
),
default_key=1,
) | python | def prompt_overwrite_json(original, new, target_path, dumps=json_dumps):
"""
Prompt end user with a diff of original and new json that may
overwrite the file at the target_path. This function only displays
a confirmation prompt and it is up to the caller to implement the
actual functionality. Optionally, a custom json.dumps method can
also be passed in for output generation.
"""
# generate compacted ndiff output.
diff = '\n'.join(l for l in (
line.rstrip() for line in difflib.ndiff(
json_dumps(original).splitlines(),
json_dumps(new).splitlines(),
))
if l[:1] in '?+-' or l[-1:] in '{}' or l[-2:] == '},')
basename_target = basename(target_path)
return prompt(
"Generated '%(basename_target)s' differs with '%(target_path)s'.\n\n"
"The following is a compacted list of changes required:\n"
"%(diff)s\n\n"
"Overwrite '%(target_path)s'?" % locals(),
choices=(
('Yes', True),
('No', False),
),
default_key=1,
) | [
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calmjs/calmjs | src/calmjs/npm.py | locate_package_entry_file | def locate_package_entry_file(working_dir, package_name):
"""
Locate a single npm package to return its browser or main entry.
"""
basedir = join(working_dir, 'node_modules', package_name)
package_json = join(basedir, 'package.json')
if not exists(package_json):
logger.debug(
"could not locate package.json for the npm package '%s' in the "
"current working directory '%s'; the package may have been "
"not installed, the build process may fail",
package_name, working_dir,
)
return
with open(package_json) as fd:
package_info = json.load(fd)
if ('browser' in package_info or 'main' in package_info):
# assume the target file exists because configuration files
# never lie /s
return join(
basedir,
*(package_info.get('browser') or package_info['main']).split('/')
)
index_js = join(basedir, 'index.js')
if exists(index_js):
return index_js
logger.debug(
"package.json for the npm package '%s' does not contain a main "
"entry point", package_name,
) | python | def locate_package_entry_file(working_dir, package_name):
"""
Locate a single npm package to return its browser or main entry.
"""
basedir = join(working_dir, 'node_modules', package_name)
package_json = join(basedir, 'package.json')
if not exists(package_json):
logger.debug(
"could not locate package.json for the npm package '%s' in the "
"current working directory '%s'; the package may have been "
"not installed, the build process may fail",
package_name, working_dir,
)
return
with open(package_json) as fd:
package_info = json.load(fd)
if ('browser' in package_info or 'main' in package_info):
# assume the target file exists because configuration files
# never lie /s
return join(
basedir,
*(package_info.get('browser') or package_info['main']).split('/')
)
index_js = join(basedir, 'index.js')
if exists(index_js):
return index_js
logger.debug(
"package.json for the npm package '%s' does not contain a main "
"entry point", package_name,
) | [
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bitlabstudio/cmsplugin-image-gallery | image_gallery/templatetags/image_gallery_tags.py | render_pictures | def render_pictures(context, selection='recent', amount=3):
"""Template tag to render a list of pictures."""
pictures = Image.objects.filter(
folder__id__in=Gallery.objects.filter(is_published=True).values_list(
'folder__pk', flat=True))
if selection == 'recent':
context.update({
'pictures': pictures.order_by('-uploaded_at')[:amount]
})
elif selection == 'random':
context.update({
'pictures': pictures.order_by('?')[:amount]
})
else:
return None
return context | python | def render_pictures(context, selection='recent', amount=3):
"""Template tag to render a list of pictures."""
pictures = Image.objects.filter(
folder__id__in=Gallery.objects.filter(is_published=True).values_list(
'folder__pk', flat=True))
if selection == 'recent':
context.update({
'pictures': pictures.order_by('-uploaded_at')[:amount]
})
elif selection == 'random':
context.update({
'pictures': pictures.order_by('?')[:amount]
})
else:
return None
return context | [
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pandeylab/pythomics | pythomics/genomics/structures.py | VCFFile.add_header | def add_header(self, entry):
"""Parses the VCF Header field and returns the number of samples in the VCF file"""
info = entry.split('\t')
self.n_individuals = len(info)-9
for i,v in enumerate(info[9:]):
self.individuals[v] = i
return self.n_individuals > 0 | python | def add_header(self, entry):
"""Parses the VCF Header field and returns the number of samples in the VCF file"""
info = entry.split('\t')
self.n_individuals = len(info)-9
for i,v in enumerate(info[9:]):
self.individuals[v] = i
return self.n_individuals > 0 | [
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pandeylab/pythomics | pythomics/genomics/structures.py | VCFFile.add_entry | def add_entry(self, row):
"""This will parse the VCF entry and also store it within the VCFFile. It will also
return the VCFEntry as well.
"""
var_call = VCFEntry(self.individuals)
var_call.parse_entry( row )
self.entries[(var_call.chrom, var_call.pos)] = var_call
return var_call | python | def add_entry(self, row):
"""This will parse the VCF entry and also store it within the VCFFile. It will also
return the VCFEntry as well.
"""
var_call = VCFEntry(self.individuals)
var_call.parse_entry( row )
self.entries[(var_call.chrom, var_call.pos)] = var_call
return var_call | [
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pandeylab/pythomics | pythomics/genomics/structures.py | VCFFile.get_header | def get_header(self, individual=-1):
"""Returns the vcf header
"""
type_map = dict([(val,key) for key,val in self.meta.type_map.iteritems()])
extra = '\n'.join(['##{0}'.format(i) for i in self.meta.extra])
info = '\n'.join(['##INFO=<ID={0},Number={1},Type={2},Description={3}>'.format(key, val.get('num_entries','.'), type_map.get(val.get('type', '')), val.get('description')) for key,val in self.meta.info.iteritems()])
filter = '\n'.join(['##FILTER=<ID={0},Description={1}>'.format(key, val.get('description','.')) for key,val in self.meta.filter.iteritems()])
format = '\n'.join(['##FORMAT=<ID={0},Number={1},Type={2},Description={3}>'.format(key, val.get('num_entries','.'), type_map.get(val.get('type', '')), val.get('description')) for key,val in self.meta.format.iteritems()])
alt = '\n'.join(['##ALT=<ID={0},Description={1}>'.format(key, val.get('description','.')) for key,val in self.meta.alt.iteritems()])
header = '\t'.join(['#CHROM','POS','ID','REF','ALT','QUAL','FILTER','INFO','FORMAT'])
if individual is not None:
if individual == -1:
individual = '\t'.join(self.individuals.keys())
else:
if isinstance(individual, int):
for i, v in self.individuals.iteritems():
if v == individual:
individual = i
break
header += '\t'+individual
return '\n'.join([extra, info, filter, format, alt, header]) | python | def get_header(self, individual=-1):
"""Returns the vcf header
"""
type_map = dict([(val,key) for key,val in self.meta.type_map.iteritems()])
extra = '\n'.join(['##{0}'.format(i) for i in self.meta.extra])
info = '\n'.join(['##INFO=<ID={0},Number={1},Type={2},Description={3}>'.format(key, val.get('num_entries','.'), type_map.get(val.get('type', '')), val.get('description')) for key,val in self.meta.info.iteritems()])
filter = '\n'.join(['##FILTER=<ID={0},Description={1}>'.format(key, val.get('description','.')) for key,val in self.meta.filter.iteritems()])
format = '\n'.join(['##FORMAT=<ID={0},Number={1},Type={2},Description={3}>'.format(key, val.get('num_entries','.'), type_map.get(val.get('type', '')), val.get('description')) for key,val in self.meta.format.iteritems()])
alt = '\n'.join(['##ALT=<ID={0},Description={1}>'.format(key, val.get('description','.')) for key,val in self.meta.alt.iteritems()])
header = '\t'.join(['#CHROM','POS','ID','REF','ALT','QUAL','FILTER','INFO','FORMAT'])
if individual is not None:
if individual == -1:
individual = '\t'.join(self.individuals.keys())
else:
if isinstance(individual, int):
for i, v in self.individuals.iteritems():
if v == individual:
individual = i
break
header += '\t'+individual
return '\n'.join([extra, info, filter, format, alt, header]) | [
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pandeylab/pythomics | pythomics/genomics/structures.py | VCFMeta.add_info | def add_info(self, entry):
"""Parse and store the info field"""
entry = entry[8:-1]
info = entry.split(',')
if len(info) < 4:
return False
for v in info:
key, value = v.split('=', 1)
if key == 'ID':
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break
return True | python | def add_info(self, entry):
"""Parse and store the info field"""
entry = entry[8:-1]
info = entry.split(',')
if len(info) < 4:
return False
for v in info:
key, value = v.split('=', 1)
if key == 'ID':
self.info[value] = {}
id_ = value
elif key == 'Number':
if value == 'A' or value == 'G':
value = -1
self.info[id_]['num_entries'] = value
elif key == 'Type':
self.info[id_]['type'] = self.type_map[value]
elif key == 'Description':
self.info[id_]['description'] = value
if len(info) > 4:
self.info[id_]['description'] += '; '.join(info[4:])
break
return True | [
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pandeylab/pythomics | pythomics/genomics/structures.py | VCFMeta.add_filter | def add_filter(self, entry):
"""Parse and store the filter field"""
entry = entry[10:-1]
info = entry.split(',')
if len(info) < 2:
return False
for v in info:
key, value = v.split('=', 1)
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return True | python | def add_filter(self, entry):
"""Parse and store the filter field"""
entry = entry[10:-1]
info = entry.split(',')
if len(info) < 2:
return False
for v in info:
key, value = v.split('=', 1)
if key == 'ID':
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id_ = value
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self.filter[id_]['description'] = value
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return True | [
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pandeylab/pythomics | pythomics/genomics/structures.py | VCFMeta.add_alt | def add_alt(self, entry):
"""Parse and store the alternative allele field"""
entry = entry[7:-1]
info = entry.split(',')
if len(info) < 2:
return False
for v in info:
key, value = v.split('=', 1)
if key == 'ID':
self.alt[value] = {}
id_ = value
elif key == 'Description':
self.alt[id_]['description'] = value
if len(info) > 4:
self.alt[id_]['description'] += '; '.join(info[4:])
break
return True | python | def add_alt(self, entry):
"""Parse and store the alternative allele field"""
entry = entry[7:-1]
info = entry.split(',')
if len(info) < 2:
return False
for v in info:
key, value = v.split('=', 1)
if key == 'ID':
self.alt[value] = {}
id_ = value
elif key == 'Description':
self.alt[id_]['description'] = value
if len(info) > 4:
self.alt[id_]['description'] += '; '.join(info[4:])
break
return True | [
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pandeylab/pythomics | pythomics/genomics/structures.py | VCFEntry.sample_string | def sample_string(self, individual=-1):
"""Returns the VCF entry as it appears in the vcf file"""
base = str(self)
extra = self.get_sample_info(individual=individual)
extra = [':'.join([str(j) for j in i]) for i in zip(*extra.values())]
return '\t'.join([base, '\t'.join(extra)]) | python | def sample_string(self, individual=-1):
"""Returns the VCF entry as it appears in the vcf file"""
base = str(self)
extra = self.get_sample_info(individual=individual)
extra = [':'.join([str(j) for j in i]) for i in zip(*extra.values())]
return '\t'.join([base, '\t'.join(extra)]) | [
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pandeylab/pythomics | pythomics/genomics/structures.py | VCFEntry.get_sample_info | def get_sample_info(self, individual=-1):
"""Returns the sample info of a given sample or all by default
"""
if isinstance(individual, str):
individual = self.individuals[individual]
extra = OrderedDict()
for format_ in self.format:
index = getattr(self, format_)
if index != -1:
if format_ == 'GT':
d = self.genotype
elif format_ == 'GQ':
d = self.genome_quality
elif format_ == 'DP':
d = self.depth
if individual == -1:
if len(d) != len(self.samples):
[self.parse_sample(i) for i in six.moves.range(len(self.samples))]
extra[format_] = [d[i] for i in six.moves.range(len(d))]
else:
if individual not in d:
self.parse_sample(individual)
extra[format_] = [d[individual]]
return extra | python | def get_sample_info(self, individual=-1):
"""Returns the sample info of a given sample or all by default
"""
if isinstance(individual, str):
individual = self.individuals[individual]
extra = OrderedDict()
for format_ in self.format:
index = getattr(self, format_)
if index != -1:
if format_ == 'GT':
d = self.genotype
elif format_ == 'GQ':
d = self.genome_quality
elif format_ == 'DP':
d = self.depth
if individual == -1:
if len(d) != len(self.samples):
[self.parse_sample(i) for i in six.moves.range(len(self.samples))]
extra[format_] = [d[i] for i in six.moves.range(len(d))]
else:
if individual not in d:
self.parse_sample(individual)
extra[format_] = [d[individual]]
return extra | [
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pandeylab/pythomics | pythomics/genomics/structures.py | VCFEntry.is_homozygous | def is_homozygous(self, individual=None):
"""This will give a boolean list corresponding to whether each individual
is homozygous for the alternative allele.
"""
if individual is not None:
if isinstance(individual, str):
individual = self.individuals[individual]
alts = self.genotype[individual]
return [sum(alts) == len(alts)] if sum(alts) > 0 else [False]
else:
return [sum(alts) == len(alts) if sum(alts) > 0 else False for i, alts in self.genotype.iteritems()] | python | def is_homozygous(self, individual=None):
"""This will give a boolean list corresponding to whether each individual
is homozygous for the alternative allele.
"""
if individual is not None:
if isinstance(individual, str):
individual = self.individuals[individual]
alts = self.genotype[individual]
return [sum(alts) == len(alts)] if sum(alts) > 0 else [False]
else:
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pandeylab/pythomics | pythomics/genomics/structures.py | VCFEntry.get_alt | def get_alt(self, individual=0, nucleotides_only=True):
"""Returns the alternative alleles of the individual as a list"""
#not i.startswith(',') is put in to handle cases like <DEL:ME:ALU> where we have no alternate allele
#but some reference
if isinstance(individual, str):
individual = self.individuals[individual]
if nucleotides_only:
return [self.alt[i-1].replace('.', '') for i in self.genotype[individual] if i > 0 and not self.alt[i-1].startswith('<')]
else:
return [self.alt[i-1].replace('.', '') for i in self.genotype[individual] if i > 0] | python | def get_alt(self, individual=0, nucleotides_only=True):
"""Returns the alternative alleles of the individual as a list"""
#not i.startswith(',') is put in to handle cases like <DEL:ME:ALU> where we have no alternate allele
#but some reference
if isinstance(individual, str):
individual = self.individuals[individual]
if nucleotides_only:
return [self.alt[i-1].replace('.', '') for i in self.genotype[individual] if i > 0 and not self.alt[i-1].startswith('<')]
else:
return [self.alt[i-1].replace('.', '') for i in self.genotype[individual] if i > 0] | [
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pandeylab/pythomics | pythomics/genomics/structures.py | VCFEntry.get_alt_length | def get_alt_length(self, individual=0):
"""Returns the number of basepairs of each alternative allele"""
if isinstance(individual, str):
individual = self.individuals[individual]
return [len(self.alt[i-1].replace('.','')) for i in self.genotype[individual] if i > 0 and not self.alt[i-1].startswith('<')] | python | def get_alt_length(self, individual=0):
"""Returns the number of basepairs of each alternative allele"""
if isinstance(individual, str):
individual = self.individuals[individual]
return [len(self.alt[i-1].replace('.','')) for i in self.genotype[individual] if i > 0 and not self.alt[i-1].startswith('<')] | [
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pandeylab/pythomics | pythomics/genomics/structures.py | VCFEntry.get_alt_lengths | def get_alt_lengths(self):
"""Returns the longest length of the variant. For deletions, return is negative,
SNPs return 0, and insertions are +. None return corresponds to no variant in interval
for specified individual
"""
#this is a hack to store the # of individuals without having to actually store it
out = []
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valid_alt = self.get_alt_length(individual=i)
if not valid_alt:
out.append(None)
else:
out.append(max(valid_alt)-len(self.ref))
return out | python | def get_alt_lengths(self):
"""Returns the longest length of the variant. For deletions, return is negative,
SNPs return 0, and insertions are +. None return corresponds to no variant in interval
for specified individual
"""
#this is a hack to store the # of individuals without having to actually store it
out = []
for i in six.moves.range(len(self.genotype)):
valid_alt = self.get_alt_length(individual=i)
if not valid_alt:
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else:
out.append(max(valid_alt)-len(self.ref))
return out | [
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pandeylab/pythomics | pythomics/genomics/structures.py | VCFEntry.has_snp | def has_snp(self, individual=0):
"""Returns a boolean list of SNP status, ordered by samples"""
if isinstance(individual, str):
individual = self.individuals[individual]
alts = self.get_alt(individual=individual)
if alts:
return [i != self.ref and len(i) == len(self.ref) for i in alts]
return [False] | python | def has_snp(self, individual=0):
"""Returns a boolean list of SNP status, ordered by samples"""
if isinstance(individual, str):
individual = self.individuals[individual]
alts = self.get_alt(individual=individual)
if alts:
return [i != self.ref and len(i) == len(self.ref) for i in alts]
return [False] | [
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pandeylab/pythomics | pythomics/genomics/structures.py | VCFEntry.parse_entry | def parse_entry(self, entry):
"""This parses a VCF row and stores the relevant information"""
entry = entry.split('\t')
self.chrom, self.pos, self.id, self.ref, alt_, self.qual, filter_, info, self.format = entry[:9]
self.samples = entry[9:]
self.alt = alt_.split(',')
if filter_ == 'PASS' or filter_ == '.':
self.passed = True
else:
self.passed = filter_.split(';')
self.info = info
# currently unused
#if info != '.':
#info_l = info.split(';')
#self.info = [v.split('=') if '=' in v else (v,1) for v in info_l]
self.format = self.format.split(':')
if 'GT' in self.format:
self.GT = self.format.index('GT')
if 'GQ' in self.format:
self.GQ = self.format.index('GQ')
if 'DP' in self.format:
self.DP = self.format.index('DP')
if 'FT' in self.format:
self.FT = self.format.index('FT') | python | def parse_entry(self, entry):
"""This parses a VCF row and stores the relevant information"""
entry = entry.split('\t')
self.chrom, self.pos, self.id, self.ref, alt_, self.qual, filter_, info, self.format = entry[:9]
self.samples = entry[9:]
self.alt = alt_.split(',')
if filter_ == 'PASS' or filter_ == '.':
self.passed = True
else:
self.passed = filter_.split(';')
self.info = info
# currently unused
#if info != '.':
#info_l = info.split(';')
#self.info = [v.split('=') if '=' in v else (v,1) for v in info_l]
self.format = self.format.split(':')
if 'GT' in self.format:
self.GT = self.format.index('GT')
if 'GQ' in self.format:
self.GQ = self.format.index('GQ')
if 'DP' in self.format:
self.DP = self.format.index('DP')
if 'FT' in self.format:
self.FT = self.format.index('FT') | [
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pandeylab/pythomics | pythomics/genomics/structures.py | GFFFeature.add_child | def add_child(self, child):
"""Children are GFFFeatures and are defined when added. This is done to avoid memory overheads
that may be incurred by GFF files that have millions of rows.
"""
child_id = getattr(child, 'id', None)
if child_id:
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if child_id not in self.children:
self.children[child_id] = child | python | def add_child(self, child):
"""Children are GFFFeatures and are defined when added. This is done to avoid memory overheads
that may be incurred by GFF files that have millions of rows.
"""
child_id = getattr(child, 'id', None)
if child_id:
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self.children[child_id] = child | [
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weso/CWR-DataApi | cwr/parser/encoder/standart/record.py | _iso_handler | def _iso_handler(obj):
"""
Transforms an object into it's ISO format, if possible.
If the object can't be transformed, then an error is raised for the JSON
parser.
This is meant to be used on datetime instances, but will work with any
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:param obj: object to transform into it's ISO format
:return: the ISO format of the object
"""
if hasattr(obj, 'isoformat'):
result = obj.isoformat()
else:
raise TypeError("Unserializable object {} of type {}".format(obj,
type(obj)))
return result | python | def _iso_handler(obj):
"""
Transforms an object into it's ISO format, if possible.
If the object can't be transformed, then an error is raised for the JSON
parser.
This is meant to be used on datetime instances, but will work with any
object having a method called isoformat.
:param obj: object to transform into it's ISO format
:return: the ISO format of the object
"""
if hasattr(obj, 'isoformat'):
result = obj.isoformat()
else:
raise TypeError("Unserializable object {} of type {}".format(obj,
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return result | [
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calmjs/calmjs | src/calmjs/runtime.py | BootstrapRuntime.argparser | def argparser(self):
"""
For setting up the argparser for this instance.
"""
if self.__argparser is None:
self.__argparser = self.argparser_factory()
self.init_argparser(self.__argparser)
return self.__argparser | python | def argparser(self):
"""
For setting up the argparser for this instance.
"""
if self.__argparser is None:
self.__argparser = self.argparser_factory()
self.init_argparser(self.__argparser)
return self.__argparser | [
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"""
Produces argparser for this type of Runtime.
"""
return ArgumentParser(
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"""
Produces argparser for this type of Runtime.
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return ArgumentParser(
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calmjs/calmjs | src/calmjs/runtime.py | Runtime.unrecognized_arguments_error | def unrecognized_arguments_error(self, args, parsed, extras):
"""
This exists because argparser is dumb and naive and doesn't
fail unrecognized arguments early.
"""
# loop variants
kwargs = vars(parsed)
failed = list(extras)
# initial values
runtime, subparser, idx = (self, self.argparser, 0)
# recursion not actually needed when it can be flattened.
while isinstance(runtime, Runtime):
cmd = kwargs.pop(runtime.action_key)
# can happen if it wasn't set, or is set but from a default
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action_idx = None if cmd not in args else args.index(cmd)
if cmd not in args and cmd is not None:
# this normally shouldn't happen, and the test case
# showed that the parsing will not flip down to the
# forced default subparser - this can remain a debug
# message until otherwise.
logger.debug(
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subparser.prog, cmd
)
subargs = args[idx:action_idx]
subparsed, subextras = subparser.parse_known_args(subargs)
if subextras:
subparser.unrecognized_arguments_error(subextras)
# since the failed arguments are in order
failed = failed[len(subextras):]
if not failed:
# have taken everything, quit now.
# also note that if cmd was really None it would
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# forced action_idx to be None which took all
# remaining tokens from failed, so definitely get
# out of here.
break
# advance the values
# note that any internal consistency will almost certainly
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details = runtime.get_argparser_details(subparser)
runtime = details.runtimes[cmd]
subparser = details.subparsers[cmd]
idx = action_idx + 1
if failed:
subparser.unrecognized_arguments_error(failed)
sys.exit(2) | python | def unrecognized_arguments_error(self, args, parsed, extras):
"""
This exists because argparser is dumb and naive and doesn't
fail unrecognized arguments early.
"""
# loop variants
kwargs = vars(parsed)
failed = list(extras)
# initial values
runtime, subparser, idx = (self, self.argparser, 0)
# recursion not actually needed when it can be flattened.
while isinstance(runtime, Runtime):
cmd = kwargs.pop(runtime.action_key)
# can happen if it wasn't set, or is set but from a default
# value (thus not provided by args)
action_idx = None if cmd not in args else args.index(cmd)
if cmd not in args and cmd is not None:
# this normally shouldn't happen, and the test case
# showed that the parsing will not flip down to the
# forced default subparser - this can remain a debug
# message until otherwise.
logger.debug(
"command for prog=%r is set to %r without being specified "
"as part of the input arguments - the following error "
"message may contain misleading references",
subparser.prog, cmd
)
subargs = args[idx:action_idx]
subparsed, subextras = subparser.parse_known_args(subargs)
if subextras:
subparser.unrecognized_arguments_error(subextras)
# since the failed arguments are in order
failed = failed[len(subextras):]
if not failed:
# have taken everything, quit now.
# also note that if cmd was really None it would
# cause KeyError below, but fortunately it also
# forced action_idx to be None which took all
# remaining tokens from failed, so definitely get
# out of here.
break
# advance the values
# note that any internal consistency will almost certainly
# result in KeyError being raised.
details = runtime.get_argparser_details(subparser)
runtime = details.runtimes[cmd]
subparser = details.subparsers[cmd]
idx = action_idx + 1
if failed:
subparser.unrecognized_arguments_error(failed)
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calmjs/calmjs | src/calmjs/runtime.py | Runtime.error | def error(self, argparser, target, message):
"""
This was used as part of the original non-recursive lookup for
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"""
warnings.warn(
'Runtime.error is deprecated and will be removed by calmjs-4.0.0',
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argparser.error(message) | python | def error(self, argparser, target, message):
"""
This was used as part of the original non-recursive lookup for
the target parser.
"""
warnings.warn(
'Runtime.error is deprecated and will be removed by calmjs-4.0.0',
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calmjs/calmjs | src/calmjs/runtime.py | ToolchainRuntime.init_argparser_working_dir | def init_argparser_working_dir(
self, argparser,
explanation='',
help_template=(
'the working directory; %(explanation)s'
'default is current working directory (%(cwd)s)'),
):
"""
Subclass could an extra expanation on how this is used.
Arguments
explanation
Explanation text for the default help template
help_template
A standard help message for this option.
"""
cwd = self.toolchain.join_cwd()
argparser.add_argument(
'--working-dir', dest=WORKING_DIR,
metavar=metavar(WORKING_DIR),
default=cwd,
help=help_template % {'explanation': explanation, 'cwd': cwd},
) | python | def init_argparser_working_dir(
self, argparser,
explanation='',
help_template=(
'the working directory; %(explanation)s'
'default is current working directory (%(cwd)s)'),
):
"""
Subclass could an extra expanation on how this is used.
Arguments
explanation
Explanation text for the default help template
help_template
A standard help message for this option.
"""
cwd = self.toolchain.join_cwd()
argparser.add_argument(
'--working-dir', dest=WORKING_DIR,
metavar=metavar(WORKING_DIR),
default=cwd,
help=help_template % {'explanation': explanation, 'cwd': cwd},
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calmjs/calmjs | src/calmjs/runtime.py | ToolchainRuntime.init_argparser_build_dir | def init_argparser_build_dir(
self, argparser, help=(
'the build directory, where all sources will be copied to '
'as part of the build process; if left unspecified, the '
'default behavior is to create a new temporary directory '
'that will be removed upon conclusion of the build; if '
'specified, it must be an existing directory and all files '
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)):
"""
For setting up build directory
"""
argparser.add_argument(
'--build-dir', default=None, dest=BUILD_DIR,
metavar=metavar(BUILD_DIR), help=help,
) | python | def init_argparser_build_dir(
self, argparser, help=(
'the build directory, where all sources will be copied to '
'as part of the build process; if left unspecified, the '
'default behavior is to create a new temporary directory '
'that will be removed upon conclusion of the build; if '
'specified, it must be an existing directory and all files '
'for the build will be copied there instead, overwriting any '
'existing file, with no cleanup done after.'
)):
"""
For setting up build directory
"""
argparser.add_argument(
'--build-dir', default=None, dest=BUILD_DIR,
metavar=metavar(BUILD_DIR), help=help,
) | [
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calmjs/calmjs | src/calmjs/runtime.py | ToolchainRuntime.init_argparser_optional_advice | def init_argparser_optional_advice(
self, argparser, default=[], help=(
'a comma separated list of packages to retrieve optional '
'advice from; the provided packages should have registered '
'the appropriate entry points for setting up the advices for '
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)):
"""
For setting up optional advice.
"""
argparser.add_argument(
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dest=ADVICE_PACKAGES, action=StoreRequirementList,
metavar='<advice>[,<advice>[...]]',
help=help
) | python | def init_argparser_optional_advice(
self, argparser, default=[], help=(
'a comma separated list of packages to retrieve optional '
'advice from; the provided packages should have registered '
'the appropriate entry points for setting up the advices for '
'the toolchain; refer to documentation for the specified '
'packages for details'
)):
"""
For setting up optional advice.
"""
argparser.add_argument(
'--optional-advice', default=default, required=False,
dest=ADVICE_PACKAGES, action=StoreRequirementList,
metavar='<advice>[,<advice>[...]]',
help=help
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calmjs/calmjs | src/calmjs/runtime.py | ToolchainRuntime.prepare_spec | def prepare_spec(self, spec, **kwargs):
"""
Prepare a spec for usage with the generic ToolchainRuntime.
Subclasses should avoid overriding this; override create_spec
instead.
"""
self.prepare_spec_debug_flag(spec, **kwargs)
self.prepare_spec_export_target_checks(spec, **kwargs)
# defer the setup till the actual toolchain invocation
spec.advise(SETUP, self.prepare_spec_advice_packages, spec, **kwargs) | python | def prepare_spec(self, spec, **kwargs):
"""
Prepare a spec for usage with the generic ToolchainRuntime.
Subclasses should avoid overriding this; override create_spec
instead.
"""
self.prepare_spec_debug_flag(spec, **kwargs)
self.prepare_spec_export_target_checks(spec, **kwargs)
# defer the setup till the actual toolchain invocation
spec.advise(SETUP, self.prepare_spec_advice_packages, spec, **kwargs) | [
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calmjs/calmjs | src/calmjs/runtime.py | ToolchainRuntime.kwargs_to_spec | def kwargs_to_spec(self, **kwargs):
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Turn the provided kwargs into arguments ready for toolchain.
"""
spec = self.create_spec(**kwargs)
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calmjs/calmjs | src/calmjs/runtime.py | BaseArtifactRegistryRuntime.init_argparser_package_names | def init_argparser_package_names(self, argparser, help=(
'names of the python package to generate artifacts for; '
'note that the metadata directory for the specified '
'packages must be writable')):
"""
Default helper for setting up the package_names option.
This is separate so that subclasses are not assumed for the
purposes of artifact creation; they should consider modifying
the default help message to reflect the fact.
"""
argparser.add_argument(
'package_names', metavar=metavar('package'), nargs='+', help=help) | python | def init_argparser_package_names(self, argparser, help=(
'names of the python package to generate artifacts for; '
'note that the metadata directory for the specified '
'packages must be writable')):
"""
Default helper for setting up the package_names option.
This is separate so that subclasses are not assumed for the
purposes of artifact creation; they should consider modifying
the default help message to reflect the fact.
"""
argparser.add_argument(
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calmjs/calmjs | src/calmjs/runtime.py | SourcePackageToolchainRuntime.init_argparser_source_registry | def init_argparser_source_registry(
self, argparser, default=None, help=(
'comma separated list of registries to use for gathering '
'JavaScript sources from the given Python packages'
)):
"""
For setting up the source registry flag.
"""
argparser.add_argument(
'--source-registry', default=default,
dest=CALMJS_MODULE_REGISTRY_NAMES, action=StoreDelimitedList,
metavar='<registry>[,<registry>[...]]',
help=help,
)
argparser.add_argument(
'--source-registries', default=default,
dest=CALMJS_MODULE_REGISTRY_NAMES, action=StoreDelimitedList,
help=SUPPRESS,
) | python | def init_argparser_source_registry(
self, argparser, default=None, help=(
'comma separated list of registries to use for gathering '
'JavaScript sources from the given Python packages'
)):
"""
For setting up the source registry flag.
"""
argparser.add_argument(
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dest=CALMJS_MODULE_REGISTRY_NAMES, action=StoreDelimitedList,
metavar='<registry>[,<registry>[...]]',
help=help,
)
argparser.add_argument(
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dest=CALMJS_MODULE_REGISTRY_NAMES, action=StoreDelimitedList,
help=SUPPRESS,
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calmjs/calmjs | src/calmjs/runtime.py | SourcePackageToolchainRuntime.init_argparser_loaderplugin_registry | def init_argparser_loaderplugin_registry(
self, argparser, default=None, help=(
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)):
"""
Default helper for setting up the loaderplugin registries flags.
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"""
argparser.add_argument(
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dest=CALMJS_LOADERPLUGIN_REGISTRY_NAME, action='store',
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help=help,
) | python | def init_argparser_loaderplugin_registry(
self, argparser, default=None, help=(
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)):
"""
Default helper for setting up the loaderplugin registries flags.
Note that this is NOT part of the init_argparser due to
implementation specific requirements. Subclasses should
consider modifying the default value help message to cater to the
toolchain it encapsulates.
"""
argparser.add_argument(
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dest=CALMJS_LOADERPLUGIN_REGISTRY_NAME, action='store',
metavar=metavar('registry'),
help=help,
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weso/CWR-DataApi | cwr/grammar/field/basic.py | _check_not_empty | def _check_not_empty(string):
"""
Checks that the string is not empty.
If it is empty an exception is raised, stopping the validation.
This is used for compulsory alphanumeric fields.
:param string: the field value
"""
string = string.strip()
if len(string) == 0:
message = 'The string should not be empty'
raise pp.ParseException(message) | python | def _check_not_empty(string):
"""
Checks that the string is not empty.
If it is empty an exception is raised, stopping the validation.
This is used for compulsory alphanumeric fields.
:param string: the field value
"""
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weso/CWR-DataApi | cwr/grammar/field/basic.py | _to_numeric_float | def _to_numeric_float(number, nums_int):
"""
Transforms a string into a float.
The nums_int parameter indicates the number of characters, starting from
the left, to be used for the integer value. All the remaining ones will be
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:return: a float created from the string
"""
index_end = len(number) - nums_int
return float(number[:nums_int] + '.' + number[-index_end:]) | python | def _to_numeric_float(number, nums_int):
"""
Transforms a string into a float.
The nums_int parameter indicates the number of characters, starting from
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] | f3b6ba8308c901b6ab87073c155c08e30692333c | https://github.com/weso/CWR-DataApi/blob/f3b6ba8308c901b6ab87073c155c08e30692333c/cwr/grammar/field/basic.py#L245-L258 | train | 45,732 |
weso/CWR-DataApi | cwr/grammar/field/basic.py | _check_above_value_float | def _check_above_value_float(string, minimum):
"""
Checks that the number parsed from the string is above a minimum.
This is used on compulsory numeric fields.
If the value is not above the minimum an exception is thrown.
:param string: the field value
:param minimum: minimum value
"""
value = float(string)
if value < minimum:
message = 'The Numeric Field value should be above %s' % minimum
raise pp.ParseException(message) | python | def _check_above_value_float(string, minimum):
"""
Checks that the number parsed from the string is above a minimum.
This is used on compulsory numeric fields.
If the value is not above the minimum an exception is thrown.
:param string: the field value
:param minimum: minimum value
"""
value = float(string)
if value < minimum:
message = 'The Numeric Field value should be above %s' % minimum
raise pp.ParseException(message) | [
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weso/CWR-DataApi | cwr/grammar/field/basic.py | _to_boolean | def _to_boolean(string):
"""
Transforms a string into a boolean value.
If a value which is not 'Y' or 'N' is received, a ParseException is thrown.
:param: string: the string to transform
:return: True if the string is 'Y', False if it is 'N'
"""
if string == 'Y':
result = True
elif string == 'N':
result = False
else:
raise pp.ParseException(string, msg='Is not a valid boolean value')
return result | python | def _to_boolean(string):
"""
Transforms a string into a boolean value.
If a value which is not 'Y' or 'N' is received, a ParseException is thrown.
:param: string: the string to transform
:return: True if the string is 'Y', False if it is 'N'
"""
if string == 'Y':
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return result | [
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weso/CWR-DataApi | cwr/grammar/field/basic.py | blank | def blank(columns=1, name=None):
"""
Creates the grammar for a blank field.
These are for constant empty strings which should be ignored, as they are
used just as fillers.
:param columns: number of columns, which is the required number of
whitespaces
:param name: name for the field
:return: grammar for the blank field
"""
if name is None:
name = 'Blank Field'
field = pp.Regex('[ ]{' + str(columns) + '}')
field.leaveWhitespace()
field.suppress()
field.setName(name)
return field | python | def blank(columns=1, name=None):
"""
Creates the grammar for a blank field.
These are for constant empty strings which should be ignored, as they are
used just as fillers.
:param columns: number of columns, which is the required number of
whitespaces
:param name: name for the field
:return: grammar for the blank field
"""
if name is None:
name = 'Blank Field'
field = pp.Regex('[ ]{' + str(columns) + '}')
field.leaveWhitespace()
field.suppress()
field.setName(name)
return field | [
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pandeylab/pythomics | pythomics/genomics/parsers.py | GFFReader.contains | def contains(self, seqid, start, end, overlap=True):
"""This returns a list of GFF objects which cover a specified location.
:param seqid: The landmark identifier (usually a chromosome)
:param start: The 1-based position of the start of the range we are querying
:param end: The 1-based position of the end of the range we are querying
:param overlap: A boolean value, if true we allow features to overlap the query range.
For instance, overlap=True with the range (5,10), will return a GFF object
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:return: A list of GFF objects
"""
d = self.positions.get(seqid,[])
if overlap:
return [gff_object for gff_start, gff_end in d
for gff_object in d[(gff_start, gff_end)]
if not (end <= gff_start or start >= gff_end)]
else:
return [gff_object for gff_start, gff_end in d
for gff_object in d[(gff_start, gff_end)]
if (gff_start <= start and gff_end >= end)] | python | def contains(self, seqid, start, end, overlap=True):
"""This returns a list of GFF objects which cover a specified location.
:param seqid: The landmark identifier (usually a chromosome)
:param start: The 1-based position of the start of the range we are querying
:param end: The 1-based position of the end of the range we are querying
:param overlap: A boolean value, if true we allow features to overlap the query range.
For instance, overlap=True with the range (5,10), will return a GFF object
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:return: A list of GFF objects
"""
d = self.positions.get(seqid,[])
if overlap:
return [gff_object for gff_start, gff_end in d
for gff_object in d[(gff_start, gff_end)]
if not (end <= gff_start or start >= gff_end)]
else:
return [gff_object for gff_start, gff_end in d
for gff_object in d[(gff_start, gff_end)]
if (gff_start <= start and gff_end >= end)] | [
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pandeylab/pythomics | pythomics/genomics/parsers.py | VCFReader.contains | def contains(self, chrom, start, end, overlap=True):
"""This returns a list of VCFEntry objects which cover a specified location.
:param chrom: The landmark identifier (usually a chromosome)
:param start: The 1-based position of the start of the range we are querying
:param end: The 1-based position of the end of the range we are querying
:param overlap: A boolean value, if true we allow features to overlap the query range.
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:return: A list of VCFEntry objects
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if not (end < vcf_start or start > vcf_end)]
else:
return [vcf_entry for vcf_start, vcf_end in d
for vcf_entry in d[(vcf_start, vcf_end)]
if (vcf_start <= start and vcf_end >= end)] | python | def contains(self, chrom, start, end, overlap=True):
"""This returns a list of VCFEntry objects which cover a specified location.
:param chrom: The landmark identifier (usually a chromosome)
:param start: The 1-based position of the start of the range we are querying
:param end: The 1-based position of the end of the range we are querying
:param overlap: A boolean value, if true we allow features to overlap the query range.
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spanning from (8,15). overlap=False will only return objects fully containing the range.
:return: A list of VCFEntry objects
"""
d = self.positions.get(chrom,[])
if overlap:
return [vcf_entry for vcf_start, vcf_end in d
for vcf_entry in d[(vcf_start, vcf_end)]
if not (end < vcf_start or start > vcf_end)]
else:
return [vcf_entry for vcf_start, vcf_end in d
for vcf_entry in d[(vcf_start, vcf_end)]
if (vcf_start <= start and vcf_end >= end)] | [
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pandeylab/pythomics | pythomics/genomics/parsers.py | VCFReader.remove_variants | def remove_variants(self, variants):
"""Remove a list of variants from the positions we are scanning"""
chroms = set([i.chrom for i in variants])
for chrom in chroms:
if self.append_chromosome:
chrom = 'chr%s' % chrom
to_delete = [pos for pos in self.positions[chrom] if pos in variants]
for pos in to_delete:
del self.positions[chrom][pos] | python | def remove_variants(self, variants):
"""Remove a list of variants from the positions we are scanning"""
chroms = set([i.chrom for i in variants])
for chrom in chroms:
if self.append_chromosome:
chrom = 'chr%s' % chrom
to_delete = [pos for pos in self.positions[chrom] if pos in variants]
for pos in to_delete:
del self.positions[chrom][pos] | [
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calmjs/calmjs | src/calmjs/loaderplugin.py | LoaderPluginHandler.generate_handler_sourcepath | def generate_handler_sourcepath(
self, toolchain, spec, loaderplugin_sourcepath):
"""
The default implementation is a recursive lookup method, which
subclasses may make use of.
Subclasses must implement this to return a mapping of modnames
the the absolute path of the desired sourcefiles. Example:
return {
'text': '/tmp/src/example_module/text/index.js',
'json': '/tmp/src/example_module/json/index.js',
}
Subclasses of this implementation must accept the same
arguments, and they should invoke this implementation via super
and merge its results (e.g. using dict.update) with one provided
by this one. Also, this implementation depends on a correct
unwrap implementation for the loaderplugin at hand, if required.
"""
# since the loaderplugin_sourcepath values is the complete
# modpath with the loader plugin, the values must be stripped
# before making use of the filtering helper function for
# grouping the inner mappings
fake_spec = {}
registry = spec.get(CALMJS_LOADERPLUGIN_REGISTRY)
if registry:
fake_spec[CALMJS_LOADERPLUGIN_REGISTRY] = registry
spec_update_sourcepath_filter_loaderplugins(fake_spec, {
self.unwrap(k): v
for k, v in loaderplugin_sourcepath.items()
}, 'current', 'nested')
result = {}
for plugin_name, sourcepath in fake_spec['nested'].items():
if sourcepath == loaderplugin_sourcepath:
logger.warning(
"loaderplugin '%s' extracted same sourcepath of while "
"locating chain loaders: %s; skipping",
self.name, sourcepath
)
continue
plugin = self.registry.get_record(plugin_name)
if not plugin:
logger.warning(
"loaderplugin '%s' from registry '%s' cannot find "
"sibling loaderplugin handler for '%s'; processing "
"may fail for the following nested/chained sources: "
"%s",
self.name, self.registry.registry_name, plugin_name,
sourcepath,
)
continue
result.update(plugin.generate_handler_sourcepath(
toolchain, spec, sourcepath))
return result | python | def generate_handler_sourcepath(
self, toolchain, spec, loaderplugin_sourcepath):
"""
The default implementation is a recursive lookup method, which
subclasses may make use of.
Subclasses must implement this to return a mapping of modnames
the the absolute path of the desired sourcefiles. Example:
return {
'text': '/tmp/src/example_module/text/index.js',
'json': '/tmp/src/example_module/json/index.js',
}
Subclasses of this implementation must accept the same
arguments, and they should invoke this implementation via super
and merge its results (e.g. using dict.update) with one provided
by this one. Also, this implementation depends on a correct
unwrap implementation for the loaderplugin at hand, if required.
"""
# since the loaderplugin_sourcepath values is the complete
# modpath with the loader plugin, the values must be stripped
# before making use of the filtering helper function for
# grouping the inner mappings
fake_spec = {}
registry = spec.get(CALMJS_LOADERPLUGIN_REGISTRY)
if registry:
fake_spec[CALMJS_LOADERPLUGIN_REGISTRY] = registry
spec_update_sourcepath_filter_loaderplugins(fake_spec, {
self.unwrap(k): v
for k, v in loaderplugin_sourcepath.items()
}, 'current', 'nested')
result = {}
for plugin_name, sourcepath in fake_spec['nested'].items():
if sourcepath == loaderplugin_sourcepath:
logger.warning(
"loaderplugin '%s' extracted same sourcepath of while "
"locating chain loaders: %s; skipping",
self.name, sourcepath
)
continue
plugin = self.registry.get_record(plugin_name)
if not plugin:
logger.warning(
"loaderplugin '%s' from registry '%s' cannot find "
"sibling loaderplugin handler for '%s'; processing "
"may fail for the following nested/chained sources: "
"%s",
self.name, self.registry.registry_name, plugin_name,
sourcepath,
)
continue
result.update(plugin.generate_handler_sourcepath(
toolchain, spec, sourcepath))
return result | [
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calmjs/calmjs | src/calmjs/loaderplugin.py | NPMLoaderPluginHandler.generate_handler_sourcepath | def generate_handler_sourcepath(
self, toolchain, spec, loaderplugin_sourcepath):
"""
Attempt to locate the plugin source; returns a mapping of
modnames to the absolute path of the located sources.
"""
# TODO calmjs-4.0.0 consider formalizing to the method instead
npm_pkg_name = (
self.node_module_pkg_name
if self.node_module_pkg_name else
self.find_node_module_pkg_name(toolchain, spec)
)
if not npm_pkg_name:
cls = type(self)
registry_name = getattr(
self.registry, 'registry_name', '<invalid_registry/handler>')
if cls is NPMLoaderPluginHandler:
logger.error(
"no npm package name specified or could be resolved for "
"loaderplugin '%s' of registry '%s'; please subclass "
"%s:%s such that the npm package name become specified",
self.name, registry_name, cls.__module__, cls.__name__,
)
else:
logger.error(
"no npm package name specified or could be resolved for "
"loaderplugin '%s' of registry '%s'; implementation of "
"%s:%s may be at fault",
self.name, registry_name, cls.__module__, cls.__name__,
)
return {}
working_dir = spec.get(WORKING_DIR, None)
if working_dir is None:
logger.info(
"attempting to derive working directory using %s, as the "
"provided spec is missing working_dir", toolchain
)
working_dir = toolchain.join_cwd()
logger.debug("deriving npm loader plugin from '%s'", working_dir)
target = locate_package_entry_file(working_dir, npm_pkg_name)
if target:
logger.debug('picked %r for loader plugin %r', target, self.name)
# use the parent recursive lookup.
result = super(
NPMLoaderPluginHandler, self).generate_handler_sourcepath(
toolchain, spec, loaderplugin_sourcepath)
result.update({self.name: target})
return result
# the expected package file is not found, use the logger to show
# why.
# Also note that any inner/chained loaders will be dropped.
if exists(join(
working_dir, 'node_modules', npm_pkg_name,
'package.json')):
logger.warning(
"'package.json' for the npm package '%s' does not contain a "
"valid entry point: sources required for loader plugin '%s' "
"cannot be included automatically; the build process may fail",
npm_pkg_name, self.name,
)
else:
logger.warning(
"could not locate 'package.json' for the npm package '%s' "
"which was specified to contain the loader plugin '%s' in the "
"current working directory '%s'; the missing package may "
"be installed by running 'npm install %s' for the mean time "
"as a workaround, though the package that owns that source "
"file that has this requirement should declare an explicit "
"dependency; the build process may fail",
npm_pkg_name, self.name, working_dir,
npm_pkg_name,
)
return {} | python | def generate_handler_sourcepath(
self, toolchain, spec, loaderplugin_sourcepath):
"""
Attempt to locate the plugin source; returns a mapping of
modnames to the absolute path of the located sources.
"""
# TODO calmjs-4.0.0 consider formalizing to the method instead
npm_pkg_name = (
self.node_module_pkg_name
if self.node_module_pkg_name else
self.find_node_module_pkg_name(toolchain, spec)
)
if not npm_pkg_name:
cls = type(self)
registry_name = getattr(
self.registry, 'registry_name', '<invalid_registry/handler>')
if cls is NPMLoaderPluginHandler:
logger.error(
"no npm package name specified or could be resolved for "
"loaderplugin '%s' of registry '%s'; please subclass "
"%s:%s such that the npm package name become specified",
self.name, registry_name, cls.__module__, cls.__name__,
)
else:
logger.error(
"no npm package name specified or could be resolved for "
"loaderplugin '%s' of registry '%s'; implementation of "
"%s:%s may be at fault",
self.name, registry_name, cls.__module__, cls.__name__,
)
return {}
working_dir = spec.get(WORKING_DIR, None)
if working_dir is None:
logger.info(
"attempting to derive working directory using %s, as the "
"provided spec is missing working_dir", toolchain
)
working_dir = toolchain.join_cwd()
logger.debug("deriving npm loader plugin from '%s'", working_dir)
target = locate_package_entry_file(working_dir, npm_pkg_name)
if target:
logger.debug('picked %r for loader plugin %r', target, self.name)
# use the parent recursive lookup.
result = super(
NPMLoaderPluginHandler, self).generate_handler_sourcepath(
toolchain, spec, loaderplugin_sourcepath)
result.update({self.name: target})
return result
# the expected package file is not found, use the logger to show
# why.
# Also note that any inner/chained loaders will be dropped.
if exists(join(
working_dir, 'node_modules', npm_pkg_name,
'package.json')):
logger.warning(
"'package.json' for the npm package '%s' does not contain a "
"valid entry point: sources required for loader plugin '%s' "
"cannot be included automatically; the build process may fail",
npm_pkg_name, self.name,
)
else:
logger.warning(
"could not locate 'package.json' for the npm package '%s' "
"which was specified to contain the loader plugin '%s' in the "
"current working directory '%s'; the missing package may "
"be installed by running 'npm install %s' for the mean time "
"as a workaround, though the package that owns that source "
"file that has this requirement should declare an explicit "
"dependency; the build process may fail",
npm_pkg_name, self.name, working_dir,
npm_pkg_name,
)
return {} | [
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weso/CWR-DataApi | cwr/parser/encoder/file.py | BaseCWRFileNameEncoder.encode | def encode(self, tag):
"""
Parses a CWR file name from a FileTag object.
The result will be a string following the format CWyynnnnsss_rrr.Vxx,
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:param tag: FileTag to parse
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# Acquires sequence number
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# If the sequence is bigger the max, it is cut
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sequence = sequence[:self._sequence_l]
# If the sequence is smaller the max, it is padded with zeroes
while len(sequence) < self._sequence_l:
sequence = '0' + sequence
# Acquires version
version = str(tag.version)
# If the version is too long only the first and last number are taken,
# to remove decimal separator
if len(version) > 2:
version = version[:1] + version[-1:]
# If the version is too short, it is padded with zeroes
while len(version) < 2:
version = '0' + version
# Acquires year
# Only the two last digits of the year are used
year = str(tag.year)[-2:]
# Acquires sender and receiver
sender = tag.sender[:3]
receiver = tag.receiver[:3]
rule = self._header + year + sequence + sender
rule = rule + self._ip_delimiter + receiver + ".V" + version
return rule | python | def encode(self, tag):
"""
Parses a CWR file name from a FileTag object.
The result will be a string following the format CWyynnnnsss_rrr.Vxx,
where the numeric sequence will have the length set on the encoder's
constructor.
:param tag: FileTag to parse
:return: a string file name parsed from the FileTag
"""
# Acquires sequence number
sequence = str(tag.sequence_n)
# If the sequence is bigger the max, it is cut
if len(sequence) > self._sequence_l:
sequence = sequence[:self._sequence_l]
# If the sequence is smaller the max, it is padded with zeroes
while len(sequence) < self._sequence_l:
sequence = '0' + sequence
# Acquires version
version = str(tag.version)
# If the version is too long only the first and last number are taken,
# to remove decimal separator
if len(version) > 2:
version = version[:1] + version[-1:]
# If the version is too short, it is padded with zeroes
while len(version) < 2:
version = '0' + version
# Acquires year
# Only the two last digits of the year are used
year = str(tag.year)[-2:]
# Acquires sender and receiver
sender = tag.sender[:3]
receiver = tag.receiver[:3]
rule = self._header + year + sequence + sender
rule = rule + self._ip_delimiter + receiver + ".V" + version
return rule | [
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weso/CWR-DataApi | cwr/parser/encoder/file.py | CwrFileEncoder.encode | def encode(self, transmission):
"""
Encodes the data, creating a CWR structure from an instance from the
domain model.
:param entity: the instance to encode
:return: a cwr string structure created from the received data
"""
data = ''
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data += self._record_encode(group.group_header)
for transaction in group.transactions:
for record in transaction:
data += self._record_encode(record)
data += self._record_encode(group.group_trailer)
data += self._record_encode(transmission.trailer)
return data | python | def encode(self, transmission):
"""
Encodes the data, creating a CWR structure from an instance from the
domain model.
:param entity: the instance to encode
:return: a cwr string structure created from the received data
"""
data = ''
data += self._record_encode(transmission.header)
for group in transmission.groups:
data += self._record_encode(group.group_header)
for transaction in group.transactions:
for record in transaction:
data += self._record_encode(record)
data += self._record_encode(group.group_trailer)
data += self._record_encode(transmission.trailer)
return data | [
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pandeylab/pythomics | pythomics/proteomics/parsers.py | MGFIterator.getScan | def getScan(self, title, peptide=None):
"""
allows random lookup
"""
if self.ra.has_key(title):
self.filename.seek(self.ra[title][0],0)
toRead = self.ra[title][1]-self.ra[title][0]
info = self.filename.read(toRead)
scan = self.parseScan(info)
else:
return None
return scan | python | def getScan(self, title, peptide=None):
"""
allows random lookup
"""
if self.ra.has_key(title):
self.filename.seek(self.ra[title][0],0)
toRead = self.ra[title][1]-self.ra[title][0]
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scan = self.parseScan(info)
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pandeylab/pythomics | pythomics/proteomics/parsers.py | MGFIterator.parseScan | def parseScan(self, scan):
"""
All input follows the BEGIN IONS row and ends before END IONS
"""
setupScan = True
foundCharge = False
foundMass = False
foundTitle = False
scanObj = ScanObject()
scanObj.ms_level = 2
for row in scan.split('\n'):
if not row:
continue
entry = row.strip().split('=')
if len(entry) >= 2:
if entry[0] == 'PEPMASS':
scanObj.mass = float(entry[1])
foundMass = True
elif entry[0] == 'CHARGE':
scanObj.charge = entry[1]
foundCharge = True
elif entry[0] == 'TITLE':
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# pos = entry[1].find(',')
# title = self.titleMap[int(entry[1][:entry[1].find(',')])]
# else:
title = '='.join(entry[1:])
foundTitle = True
scanObj.title = title
scanObj.id = title
elif entry[0] == 'RTINSECONDS':
scanObj.rt = float(entry[1])
else:
mz,intensity = self.scanSplit.split(row.strip())
scanObj.scans.append((float(mz),float(intensity)))
if foundCharge and foundMass and foundTitle:
return scanObj
return None | python | def parseScan(self, scan):
"""
All input follows the BEGIN IONS row and ends before END IONS
"""
setupScan = True
foundCharge = False
foundMass = False
foundTitle = False
scanObj = ScanObject()
scanObj.ms_level = 2
for row in scan.split('\n'):
if not row:
continue
entry = row.strip().split('=')
if len(entry) >= 2:
if entry[0] == 'PEPMASS':
scanObj.mass = float(entry[1])
foundMass = True
elif entry[0] == 'CHARGE':
scanObj.charge = entry[1]
foundCharge = True
elif entry[0] == 'TITLE':
# if self.titleMap:
# pos = entry[1].find(',')
# title = self.titleMap[int(entry[1][:entry[1].find(',')])]
# else:
title = '='.join(entry[1:])
foundTitle = True
scanObj.title = title
scanObj.id = title
elif entry[0] == 'RTINSECONDS':
scanObj.rt = float(entry[1])
else:
mz,intensity = self.scanSplit.split(row.strip())
scanObj.scans.append((float(mz),float(intensity)))
if foundCharge and foundMass and foundTitle:
return scanObj
return None | [
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calmjs/calmjs | src/calmjs/artifact.py | _cls_lookup_dist | def _cls_lookup_dist(cls):
"""
Attempt to resolve the distribution from the provided class in the
most naive way - this assumes the Python module path to the class
contains the name of the package that provided the module and class.
"""
frags = cls.__module__.split('.')
for name in ('.'.join(frags[:x]) for x in range(len(frags), 0, -1)):
dist = find_pkg_dist(name)
if dist:
return dist | python | def _cls_lookup_dist(cls):
"""
Attempt to resolve the distribution from the provided class in the
most naive way - this assumes the Python module path to the class
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"""
frags = cls.__module__.split('.')
for name in ('.'.join(frags[:x]) for x in range(len(frags), 0, -1)):
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if dist:
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calmjs/calmjs | src/calmjs/artifact.py | verify_builder | def verify_builder(builder):
"""
To ensure that the provided builder has a signature that is at least
compatible.
"""
try:
d = getcallargs(builder, package_names=[], export_target='some_path')
except TypeError:
return False
return d == {'package_names': [], 'export_target': 'some_path'} | python | def verify_builder(builder):
"""
To ensure that the provided builder has a signature that is at least
compatible.
"""
try:
d = getcallargs(builder, package_names=[], export_target='some_path')
except TypeError:
return False
return d == {'package_names': [], 'export_target': 'some_path'} | [
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calmjs/calmjs | src/calmjs/artifact.py | extract_builder_result | def extract_builder_result(builder_result, toolchain_cls=Toolchain):
"""
Extract the builder result to produce a ``Toolchain`` and ``Spec``
instance.
"""
try:
toolchain, spec = builder_result
except Exception:
return None, None
if not isinstance(toolchain, toolchain_cls) or not isinstance(spec, Spec):
return None, None
return toolchain, spec | python | def extract_builder_result(builder_result, toolchain_cls=Toolchain):
"""
Extract the builder result to produce a ``Toolchain`` and ``Spec``
instance.
"""
try:
toolchain, spec = builder_result
except Exception:
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if not isinstance(toolchain, toolchain_cls) or not isinstance(spec, Spec):
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return toolchain, spec | [
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calmjs/calmjs | src/calmjs/artifact.py | trace_toolchain | def trace_toolchain(toolchain):
"""
Trace the versions of the involved packages for the provided
toolchain instance.
"""
pkgs = []
for cls in getmro(type(toolchain)):
if not issubclass(cls, Toolchain):
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dist = _cls_lookup_dist(cls)
value = {
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} if dist else {}
key = '%s:%s' % (cls.__module__, cls.__name__)
pkgs.append({key: value})
return pkgs | python | def trace_toolchain(toolchain):
"""
Trace the versions of the involved packages for the provided
toolchain instance.
"""
pkgs = []
for cls in getmro(type(toolchain)):
if not issubclass(cls, Toolchain):
continue
dist = _cls_lookup_dist(cls)
value = {
'project_name': dist.project_name,
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} if dist else {}
key = '%s:%s' % (cls.__module__, cls.__name__)
pkgs.append({key: value})
return pkgs | [
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calmjs/calmjs | src/calmjs/artifact.py | BaseArtifactRegistry.get_artifact_filename | def get_artifact_filename(self, package_name, artifact_name):
"""
Similar to pkg_resources.resource_filename, however this works
with the information cached in this registry instance, and
arguments are not quite the same.
Arguments:
package_name
The name of the package to get the artifact from
artifact_name
The exact name of the artifact.
Returns the path of where the artifact should be if it has been
declared, otherwise None.
"""
project_name = self.packages.normalize(package_name)
return self.records.get((project_name, artifact_name)) | python | def get_artifact_filename(self, package_name, artifact_name):
"""
Similar to pkg_resources.resource_filename, however this works
with the information cached in this registry instance, and
arguments are not quite the same.
Arguments:
package_name
The name of the package to get the artifact from
artifact_name
The exact name of the artifact.
Returns the path of where the artifact should be if it has been
declared, otherwise None.
"""
project_name = self.packages.normalize(package_name)
return self.records.get((project_name, artifact_name)) | [
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calmjs/calmjs | src/calmjs/artifact.py | BaseArtifactRegistry.resolve_artifacts_by_builder_compat | def resolve_artifacts_by_builder_compat(
self, package_names, builder_name, dependencies=False):
"""
Yield the list of paths to the artifacts in the order of the
dependency resolution
Arguments:
package_names
The names of the packages to probe the dependency graph, to
be provided as a list of strings.
artifact_name
The exact name of the artifact.
dependencies
Trace dependencies. Default is off.
Returns the path of where the artifact should be if it has been
declared, otherwise None.
"""
paths = self.compat_builders.get(builder_name)
if not paths:
# perhaps warn, but just return
return
resolver = (
# traces dependencies for distribution.
find_packages_requirements_dists
if dependencies else
# just get grabs the distribution.
pkg_names_to_dists
)
for distribution in resolver(package_names):
path = paths.get(distribution.project_name)
if path:
yield path | python | def resolve_artifacts_by_builder_compat(
self, package_names, builder_name, dependencies=False):
"""
Yield the list of paths to the artifacts in the order of the
dependency resolution
Arguments:
package_names
The names of the packages to probe the dependency graph, to
be provided as a list of strings.
artifact_name
The exact name of the artifact.
dependencies
Trace dependencies. Default is off.
Returns the path of where the artifact should be if it has been
declared, otherwise None.
"""
paths = self.compat_builders.get(builder_name)
if not paths:
# perhaps warn, but just return
return
resolver = (
# traces dependencies for distribution.
find_packages_requirements_dists
if dependencies else
# just get grabs the distribution.
pkg_names_to_dists
)
for distribution in resolver(package_names):
path = paths.get(distribution.project_name)
if path:
yield path | [
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The names of the packages to probe the dependency graph, to
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artifact_name
The exact name of the artifact.
dependencies
Trace dependencies. Default is off.
Returns the path of where the artifact should be if it has been
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calmjs/calmjs | src/calmjs/artifact.py | BaseArtifactRegistry.get_artifact_metadata | def get_artifact_metadata(self, package_name):
"""
Return metadata of the artifacts built through this registry.
"""
filename = self.metadata.get(package_name)
if not filename or not exists(filename):
return {}
with open(filename, encoding='utf8') as fd:
contents = fd.read()
try:
is_json_compat(contents)
except ValueError:
logger.info("artifact metadata file '%s' is invalid", filename)
return {}
return json.loads(contents) | python | def get_artifact_metadata(self, package_name):
"""
Return metadata of the artifacts built through this registry.
"""
filename = self.metadata.get(package_name)
if not filename or not exists(filename):
return {}
with open(filename, encoding='utf8') as fd:
contents = fd.read()
try:
is_json_compat(contents)
except ValueError:
logger.info("artifact metadata file '%s' is invalid", filename)
return {}
return json.loads(contents) | [
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calmjs/calmjs | src/calmjs/artifact.py | BaseArtifactRegistry.generate_metadata_entry | def generate_metadata_entry(self, entry_point, toolchain, spec):
"""
After the toolchain and spec have been executed, this may be
called to generate the artifact export entry for persistence
into the metadata file.
"""
export_target = spec['export_target']
toolchain_bases = trace_toolchain(toolchain)
toolchain_bin_path = spec.get(TOOLCHAIN_BIN_PATH)
toolchain_bin = ([
basename(toolchain_bin_path), # bin_name
get_bin_version_str(toolchain_bin_path), # bin_version
] if toolchain_bin_path else [])
return {basename(export_target): {
'toolchain_bases': toolchain_bases,
'toolchain_bin': toolchain_bin,
'builder': '%s:%s' % (
entry_point.module_name, '.'.join(entry_point.attrs)),
}} | python | def generate_metadata_entry(self, entry_point, toolchain, spec):
"""
After the toolchain and spec have been executed, this may be
called to generate the artifact export entry for persistence
into the metadata file.
"""
export_target = spec['export_target']
toolchain_bases = trace_toolchain(toolchain)
toolchain_bin_path = spec.get(TOOLCHAIN_BIN_PATH)
toolchain_bin = ([
basename(toolchain_bin_path), # bin_name
get_bin_version_str(toolchain_bin_path), # bin_version
] if toolchain_bin_path else [])
return {basename(export_target): {
'toolchain_bases': toolchain_bases,
'toolchain_bin': toolchain_bin,
'builder': '%s:%s' % (
entry_point.module_name, '.'.join(entry_point.attrs)),
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calmjs/calmjs | src/calmjs/artifact.py | BaseArtifactRegistry.iter_records_for | def iter_records_for(self, package_name):
"""
Iterate records for a specific package.
"""
entry_points = self.packages.get(package_name, NotImplemented)
if entry_points is NotImplemented:
logger.debug(
"package '%s' has not declared any entry points for the '%s' "
"registry for artifact construction",
package_name, self.registry_name,
)
return iter([])
logger.debug(
"package '%s' has declared %d entry points for the '%s' "
"registry for artifact construction",
package_name, len(entry_points), self.registry_name,
)
return iter(entry_points.values()) | python | def iter_records_for(self, package_name):
"""
Iterate records for a specific package.
"""
entry_points = self.packages.get(package_name, NotImplemented)
if entry_points is NotImplemented:
logger.debug(
"package '%s' has not declared any entry points for the '%s' "
"registry for artifact construction",
package_name, self.registry_name,
)
return iter([])
logger.debug(
"package '%s' has declared %d entry points for the '%s' "
"registry for artifact construction",
package_name, len(entry_points), self.registry_name,
)
return iter(entry_points.values()) | [
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calmjs/calmjs | src/calmjs/artifact.py | BaseArtifactRegistry.generate_builder | def generate_builder(self, entry_point, export_target):
"""
Yields exactly one builder if both the provided entry point and
export target satisfies the checks required.
"""
try:
builder = entry_point.resolve()
except ImportError:
logger.error(
"unable to import the target builder for the entry point "
"'%s' from package '%s' to generate artifact '%s'",
entry_point, entry_point.dist, export_target,
)
return
if not self.verify_builder(builder):
logger.error(
"the builder referenced by the entry point '%s' "
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entry_point, entry_point.dist,
)
return
# CLEANUP see deprecation notice below
verifier = self.verify_export_target(export_target)
if not verifier:
logger.error(
"the export target '%s' has been rejected", export_target)
return
toolchain, spec = self.extract_builder_result(builder(
[entry_point.dist.project_name], export_target=export_target))
if not toolchain:
logger.error(
"the builder referenced by the entry point '%s' "
"from package '%s' failed to produce a valid "
"toolchain",
entry_point, entry_point.dist,
)
return
if spec.get(EXPORT_TARGET) != export_target:
logger.error(
"the builder referenced by the entry point '%s' "
"from package '%s' failed to produce a spec with the "
"expected export_target",
entry_point, entry_point.dist,
)
return
if callable(verifier):
warnings.warn(
"%s:%s.verify_export_target returned a callable, which "
"will no longer be passed to spec.advise by calmjs-4.0.0; "
"please instead override 'setup_export_location' or "
"'prepare_export_location' in that class" % (
self.__class__.__module__, self.__class__.__name__),
DeprecationWarning
)
spec.advise(BEFORE_PREPARE, verifier, export_target)
else:
spec.advise(
BEFORE_PREPARE,
self.prepare_export_location, export_target)
yield entry_point, toolchain, spec | python | def generate_builder(self, entry_point, export_target):
"""
Yields exactly one builder if both the provided entry point and
export target satisfies the checks required.
"""
try:
builder = entry_point.resolve()
except ImportError:
logger.error(
"unable to import the target builder for the entry point "
"'%s' from package '%s' to generate artifact '%s'",
entry_point, entry_point.dist, export_target,
)
return
if not self.verify_builder(builder):
logger.error(
"the builder referenced by the entry point '%s' "
"from package '%s' has an incompatible signature",
entry_point, entry_point.dist,
)
return
# CLEANUP see deprecation notice below
verifier = self.verify_export_target(export_target)
if not verifier:
logger.error(
"the export target '%s' has been rejected", export_target)
return
toolchain, spec = self.extract_builder_result(builder(
[entry_point.dist.project_name], export_target=export_target))
if not toolchain:
logger.error(
"the builder referenced by the entry point '%s' "
"from package '%s' failed to produce a valid "
"toolchain",
entry_point, entry_point.dist,
)
return
if spec.get(EXPORT_TARGET) != export_target:
logger.error(
"the builder referenced by the entry point '%s' "
"from package '%s' failed to produce a spec with the "
"expected export_target",
entry_point, entry_point.dist,
)
return
if callable(verifier):
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"will no longer be passed to spec.advise by calmjs-4.0.0; "
"please instead override 'setup_export_location' or "
"'prepare_export_location' in that class" % (
self.__class__.__module__, self.__class__.__name__),
DeprecationWarning
)
spec.advise(BEFORE_PREPARE, verifier, export_target)
else:
spec.advise(
BEFORE_PREPARE,
self.prepare_export_location, export_target)
yield entry_point, toolchain, spec | [
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calmjs/calmjs | src/calmjs/artifact.py | BaseArtifactRegistry.execute_builder | def execute_builder(self, entry_point, toolchain, spec):
"""
Accepts the arguments provided by the builder and executes them.
"""
toolchain(spec)
if not exists(spec['export_target']):
logger.error(
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)
return {}
return self.generate_metadata_entry(entry_point, toolchain, spec) | python | def execute_builder(self, entry_point, toolchain, spec):
"""
Accepts the arguments provided by the builder and executes them.
"""
toolchain(spec)
if not exists(spec['export_target']):
logger.error(
"the entry point '%s' from package '%s' failed to "
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)
return {}
return self.generate_metadata_entry(entry_point, toolchain, spec) | [
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calmjs/calmjs | src/calmjs/artifact.py | ArtifactRegistry.process_package | def process_package(self, package_name):
"""
Build artifacts declared for the given package.
"""
metadata = super(ArtifactRegistry, self).process_package(package_name)
if metadata:
self.update_artifact_metadata(package_name, metadata) | python | def process_package(self, package_name):
"""
Build artifacts declared for the given package.
"""
metadata = super(ArtifactRegistry, self).process_package(package_name)
if metadata:
self.update_artifact_metadata(package_name, metadata) | [
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weso/CWR-DataApi | cwr/grammar/field/filename.py | alphanum_variable | def alphanum_variable(min_size, max_size, name=None):
"""
Creates the grammar for an alphanumeric code where the size ranges between
two values.
:param min_size: minimum size
:param max_size: maximum size
:param name: name for the field
:return: grammar for an alphanumeric field of a variable size
"""
if name is None:
name = 'Alphanumeric Field'
if min_size < 0:
# Can't have negative min
raise BaseException()
if max_size < min_size:
# Max can't be lower than min
raise BaseException()
field = pp.Word(pp.alphanums, min=min_size, max=max_size)
# Parse action
field.setParseAction(lambda s: s[0].strip())
# White spaces are not removed
field.leaveWhitespace()
# Name
field.setName(name)
return field | python | def alphanum_variable(min_size, max_size, name=None):
"""
Creates the grammar for an alphanumeric code where the size ranges between
two values.
:param min_size: minimum size
:param max_size: maximum size
:param name: name for the field
:return: grammar for an alphanumeric field of a variable size
"""
if name is None:
name = 'Alphanumeric Field'
if min_size < 0:
# Can't have negative min
raise BaseException()
if max_size < min_size:
# Max can't be lower than min
raise BaseException()
field = pp.Word(pp.alphanums, min=min_size, max=max_size)
# Parse action
field.setParseAction(lambda s: s[0].strip())
# White spaces are not removed
field.leaveWhitespace()
# Name
field.setName(name)
return field | [
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weso/CWR-DataApi | cwr/grammar/field/filename.py | year | def year(columns, name=None):
"""
Creates the grammar for a field containing a year.
:param columns: the number of columns for the year
:param name: the name of the field
:return:
"""
if columns < 0:
# Can't have negative size
raise BaseException()
field = numeric(columns, name)
# Parse action
field.addParseAction(_to_year)
return field | python | def year(columns, name=None):
"""
Creates the grammar for a field containing a year.
:param columns: the number of columns for the year
:param name: the name of the field
:return:
"""
if columns < 0:
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return field | [
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calmjs/calmjs | src/calmjs/dist.py | is_json_compat | def is_json_compat(value):
"""
Check that the value is either a JSON decodable string or a dict
that can be encoded into a JSON.
Raises ValueError when validation fails.
"""
try:
value = json.loads(value)
except ValueError as e:
raise ValueError('JSON decoding error: ' + str(e))
except TypeError:
# Check that the value can be serialized back into json.
try:
json.dumps(value)
except TypeError as e:
raise ValueError(
'must be a JSON serializable object: ' + str(e))
if not isinstance(value, dict):
raise ValueError(
'must be specified as a JSON serializable dict or a '
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)
return True | python | def is_json_compat(value):
"""
Check that the value is either a JSON decodable string or a dict
that can be encoded into a JSON.
Raises ValueError when validation fails.
"""
try:
value = json.loads(value)
except ValueError as e:
raise ValueError('JSON decoding error: ' + str(e))
except TypeError:
# Check that the value can be serialized back into json.
try:
json.dumps(value)
except TypeError as e:
raise ValueError(
'must be a JSON serializable object: ' + str(e))
if not isinstance(value, dict):
raise ValueError(
'must be specified as a JSON serializable dict or a '
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)
return True | [
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calmjs/calmjs | src/calmjs/dist.py | validate_json_field | def validate_json_field(dist, attr, value):
"""
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"""
try:
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except ValueError as e:
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"""
Check for json validity.
"""
try:
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raise DistutilsSetupError("%r %s" % (attr, e))
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calmjs/calmjs | src/calmjs/dist.py | validate_line_list | def validate_line_list(dist, attr, value):
"""
Validate that the value is compatible
"""
# does not work as reliably in Python 2.
if isinstance(value, str):
value = value.split()
value = list(value)
try:
check = (' '.join(value)).split()
if check == value:
return True
except Exception:
pass
raise DistutilsSetupError("%r must be a list of valid identifiers" % attr) | python | def validate_line_list(dist, attr, value):
"""
Validate that the value is compatible
"""
# does not work as reliably in Python 2.
if isinstance(value, str):
value = value.split()
value = list(value)
try:
check = (' '.join(value)).split()
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return True
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raise DistutilsSetupError("%r must be a list of valid identifiers" % attr) | [
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calmjs/calmjs | src/calmjs/dist.py | write_json_file | def write_json_file(argname, cmd, basename, filename):
"""
Write JSON captured from the defined argname into the package's
egg-info directory using the specified filename.
"""
value = getattr(cmd.distribution, argname, None)
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cmd.write_or_delete_file(argname, filename, value, force=True) | python | def write_json_file(argname, cmd, basename, filename):
"""
Write JSON captured from the defined argname into the package's
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"""
value = getattr(cmd.distribution, argname, None)
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calmjs/calmjs | src/calmjs/dist.py | write_line_list | def write_line_list(argname, cmd, basename, filename):
"""
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"""
Write out the retrieved value as list of lines.
"""
values = getattr(cmd.distribution, argname, None)
if isinstance(values, list):
values = '\n'.join(values)
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calmjs/calmjs | src/calmjs/dist.py | find_pkg_dist | def find_pkg_dist(pkg_name, working_set=None):
"""
Locate a package's distribution by its name.
"""
working_set = working_set or default_working_set
req = Requirement.parse(pkg_name)
return working_set.find(req) | python | def find_pkg_dist(pkg_name, working_set=None):
"""
Locate a package's distribution by its name.
"""
working_set = working_set or default_working_set
req = Requirement.parse(pkg_name)
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calmjs/calmjs | src/calmjs/dist.py | convert_package_names | def convert_package_names(package_names):
"""
Convert package names, which can be a string of a number of package
names or requirements separated by spaces.
"""
results = []
errors = []
for name in (
package_names.split()
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errors.append(name)
else:
results.append(name)
return results, errors | python | def convert_package_names(package_names):
"""
Convert package names, which can be a string of a number of package
names or requirements separated by spaces.
"""
results = []
errors = []
for name in (
package_names.split()
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try:
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errors.append(name)
else:
results.append(name)
return results, errors | [
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calmjs/calmjs | src/calmjs/dist.py | find_packages_requirements_dists | def find_packages_requirements_dists(pkg_names, working_set=None):
"""
Return the entire list of dependency requirements, reversed from the
bottom.
"""
working_set = working_set or default_working_set
requirements = [
r for r in (Requirement.parse(req) for req in pkg_names)
if working_set.find(r)
]
return list(reversed(working_set.resolve(requirements))) | python | def find_packages_requirements_dists(pkg_names, working_set=None):
"""
Return the entire list of dependency requirements, reversed from the
bottom.
"""
working_set = working_set or default_working_set
requirements = [
r for r in (Requirement.parse(req) for req in pkg_names)
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return list(reversed(working_set.resolve(requirements))) | [
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calmjs/calmjs | src/calmjs/dist.py | find_packages_parents_requirements_dists | def find_packages_parents_requirements_dists(pkg_names, working_set=None):
"""
Leverages the `find_packages_requirements_dists` but strip out the
distributions that matches pkg_names.
"""
dists = []
# opting for a naive implementation
targets = set(pkg_names)
for dist in find_packages_requirements_dists(pkg_names, working_set):
if dist.project_name in targets:
continue
dists.append(dist)
return dists | python | def find_packages_parents_requirements_dists(pkg_names, working_set=None):
"""
Leverages the `find_packages_requirements_dists` but strip out the
distributions that matches pkg_names.
"""
dists = []
# opting for a naive implementation
targets = set(pkg_names)
for dist in find_packages_requirements_dists(pkg_names, working_set):
if dist.project_name in targets:
continue
dists.append(dist)
return dists | [
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calmjs/calmjs | src/calmjs/dist.py | read_dist_egginfo_json | def read_dist_egginfo_json(dist, filename=DEFAULT_JSON):
"""
Safely get a json within an egginfo from a distribution.
"""
# use the given package's distribution to acquire the json file.
if not dist.has_metadata(filename):
logger.debug("no '%s' for '%s'", filename, dist)
return
try:
result = dist.get_metadata(filename)
except IOError:
logger.error("I/O error on reading of '%s' for '%s'.", filename, dist)
return
try:
obj = json.loads(result)
except (TypeError, ValueError):
logger.error(
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return
logger.debug("found '%s' for '%s'.", filename, dist)
return obj | python | def read_dist_egginfo_json(dist, filename=DEFAULT_JSON):
"""
Safely get a json within an egginfo from a distribution.
"""
# use the given package's distribution to acquire the json file.
if not dist.has_metadata(filename):
logger.debug("no '%s' for '%s'", filename, dist)
return
try:
result = dist.get_metadata(filename)
except IOError:
logger.error("I/O error on reading of '%s' for '%s'.", filename, dist)
return
try:
obj = json.loads(result)
except (TypeError, ValueError):
logger.error(
"the '%s' found in '%s' is not a valid json.", filename, dist)
return
logger.debug("found '%s' for '%s'.", filename, dist)
return obj | [
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calmjs/calmjs | src/calmjs/dist.py | read_egginfo_json | def read_egginfo_json(pkg_name, filename=DEFAULT_JSON, working_set=None):
"""
Read json from egginfo of a package identified by `pkg_name` that's
already installed within the current Python environment.
"""
working_set = working_set or default_working_set
dist = find_pkg_dist(pkg_name, working_set=working_set)
return read_dist_egginfo_json(dist, filename) | python | def read_egginfo_json(pkg_name, filename=DEFAULT_JSON, working_set=None):
"""
Read json from egginfo of a package identified by `pkg_name` that's
already installed within the current Python environment.
"""
working_set = working_set or default_working_set
dist = find_pkg_dist(pkg_name, working_set=working_set)
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calmjs/calmjs | src/calmjs/dist.py | flatten_dist_egginfo_json | def flatten_dist_egginfo_json(
source_dists, filename=DEFAULT_JSON, dep_keys=DEP_KEYS,
working_set=None):
"""
Flatten a distribution's egginfo json, with the depended keys to be
flattened.
Originally this was done for this:
Resolve a distribution's (dev)dependencies through the working set
and generate a flattened version package.json, returned as a dict,
from the resolved distributions.
Default working set is the one from pkg_resources.
The generated package.json dict is done by grabbing all package.json
metadata from all parent Python packages, starting from the highest
level and down to the lowest. The current distribution's
dependencies will be layered on top along with its other package
information. This has the effect of child packages overriding
node/npm dependencies which is by the design of this function. If
nested dependencies are desired, just rely on npm only for all
dependency management.
Flat is better than nested.
"""
working_set = working_set or default_working_set
obj = {}
# TODO figure out the best way to explicitly report back to caller
# how the keys came to be (from which dist). Perhaps create a
# detailed function based on this, retain this one to return the
# distilled results.
depends = {dep: {} for dep in dep_keys}
# Go from the earliest package down to the latest one, as we will
# flatten children's d(evD)ependencies on top of parent's.
for dist in source_dists:
obj = read_dist_egginfo_json(dist, filename)
if not obj:
continue
logger.debug("merging '%s' for required '%s'", filename, dist)
for dep in dep_keys:
depends[dep].update(obj.get(dep, {}))
if obj is None:
# top level object does not have egg-info defined
return depends
for dep in dep_keys:
# filtering out all the nulls.
obj[dep] = {k: v for k, v in depends[dep].items() if v is not None}
return obj | python | def flatten_dist_egginfo_json(
source_dists, filename=DEFAULT_JSON, dep_keys=DEP_KEYS,
working_set=None):
"""
Flatten a distribution's egginfo json, with the depended keys to be
flattened.
Originally this was done for this:
Resolve a distribution's (dev)dependencies through the working set
and generate a flattened version package.json, returned as a dict,
from the resolved distributions.
Default working set is the one from pkg_resources.
The generated package.json dict is done by grabbing all package.json
metadata from all parent Python packages, starting from the highest
level and down to the lowest. The current distribution's
dependencies will be layered on top along with its other package
information. This has the effect of child packages overriding
node/npm dependencies which is by the design of this function. If
nested dependencies are desired, just rely on npm only for all
dependency management.
Flat is better than nested.
"""
working_set = working_set or default_working_set
obj = {}
# TODO figure out the best way to explicitly report back to caller
# how the keys came to be (from which dist). Perhaps create a
# detailed function based on this, retain this one to return the
# distilled results.
depends = {dep: {} for dep in dep_keys}
# Go from the earliest package down to the latest one, as we will
# flatten children's d(evD)ependencies on top of parent's.
for dist in source_dists:
obj = read_dist_egginfo_json(dist, filename)
if not obj:
continue
logger.debug("merging '%s' for required '%s'", filename, dist)
for dep in dep_keys:
depends[dep].update(obj.get(dep, {}))
if obj is None:
# top level object does not have egg-info defined
return depends
for dep in dep_keys:
# filtering out all the nulls.
obj[dep] = {k: v for k, v in depends[dep].items() if v is not None}
return obj | [
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calmjs/calmjs | src/calmjs/dist.py | flatten_egginfo_json | def flatten_egginfo_json(
pkg_names, filename=DEFAULT_JSON, dep_keys=DEP_KEYS, working_set=None):
"""
A shorthand calling convention where the package name is supplied
instead of a distribution.
Originally written for this:
Generate a flattened package.json with packages `pkg_names` that are
already installed within the current Python environment (defaults
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"""
working_set = working_set or default_working_set
# Ensure only grabbing packages that exists in working_set
dists = find_packages_requirements_dists(
pkg_names, working_set=working_set)
return flatten_dist_egginfo_json(
dists, filename=filename, dep_keys=dep_keys, working_set=working_set) | python | def flatten_egginfo_json(
pkg_names, filename=DEFAULT_JSON, dep_keys=DEP_KEYS, working_set=None):
"""
A shorthand calling convention where the package name is supplied
instead of a distribution.
Originally written for this:
Generate a flattened package.json with packages `pkg_names` that are
already installed within the current Python environment (defaults
to the current global working_set which should have been set up
correctly by pkg_resources).
"""
working_set = working_set or default_working_set
# Ensure only grabbing packages that exists in working_set
dists = find_packages_requirements_dists(
pkg_names, working_set=working_set)
return flatten_dist_egginfo_json(
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] | b9b407c2b6a7662da64bccba93bb8d92e7a5fafd | https://github.com/calmjs/calmjs/blob/b9b407c2b6a7662da64bccba93bb8d92e7a5fafd/src/calmjs/dist.py#L304-L323 | train | 45,771 |
calmjs/calmjs | src/calmjs/dist.py | build_helpers_egginfo_json | def build_helpers_egginfo_json(
json_field, json_key_registry, json_filename=None):
"""
Return a tuple of functions that will provide the usage of the
JSON egginfo based around the provided field.
"""
json_filename = (
json_field + '.json' if json_filename is None else json_filename)
# Default calmjs core implementation specific functions, to be used by
# integrators intended to use this as a distribution.
def get_extras_json(pkg_names, working_set=None):
"""
Only extract the extras_json information for the given packages
'pkg_names'.
"""
working_set = working_set or default_working_set
dep_keys = set(get(json_key_registry).iter_records())
dists = pkg_names_to_dists(pkg_names, working_set=working_set)
return flatten_dist_egginfo_json(
dists, filename=json_filename,
dep_keys=dep_keys, working_set=working_set
)
def _flatten_extras_json(pkg_names, find_dists, working_set):
# registry key must be explicit here as it was designed for this.
dep_keys = set(get(json_key_registry).iter_records())
dists = find_dists(pkg_names, working_set=working_set)
return flatten_dist_egginfo_json(
dists, filename=json_filename,
dep_keys=dep_keys, working_set=working_set
)
def flatten_extras_json(pkg_names, working_set=None):
"""
Traverses through the dependency graph of packages 'pkg_names'
and flattens all the egg_info json information
"""
working_set = working_set or default_working_set
return _flatten_extras_json(
pkg_names, find_packages_requirements_dists, working_set)
def flatten_parents_extras_json(pkg_names, working_set=None):
"""
Traverses through the dependency graph of packages 'pkg_names'
and flattens all the egg_info json information for parents of
the specified packages.
"""
working_set = working_set or default_working_set
return _flatten_extras_json(
pkg_names, find_packages_parents_requirements_dists, working_set)
write_extras_json = partial(write_json_file, json_field)
return (
get_extras_json,
flatten_extras_json,
flatten_parents_extras_json,
write_extras_json,
) | python | def build_helpers_egginfo_json(
json_field, json_key_registry, json_filename=None):
"""
Return a tuple of functions that will provide the usage of the
JSON egginfo based around the provided field.
"""
json_filename = (
json_field + '.json' if json_filename is None else json_filename)
# Default calmjs core implementation specific functions, to be used by
# integrators intended to use this as a distribution.
def get_extras_json(pkg_names, working_set=None):
"""
Only extract the extras_json information for the given packages
'pkg_names'.
"""
working_set = working_set or default_working_set
dep_keys = set(get(json_key_registry).iter_records())
dists = pkg_names_to_dists(pkg_names, working_set=working_set)
return flatten_dist_egginfo_json(
dists, filename=json_filename,
dep_keys=dep_keys, working_set=working_set
)
def _flatten_extras_json(pkg_names, find_dists, working_set):
# registry key must be explicit here as it was designed for this.
dep_keys = set(get(json_key_registry).iter_records())
dists = find_dists(pkg_names, working_set=working_set)
return flatten_dist_egginfo_json(
dists, filename=json_filename,
dep_keys=dep_keys, working_set=working_set
)
def flatten_extras_json(pkg_names, working_set=None):
"""
Traverses through the dependency graph of packages 'pkg_names'
and flattens all the egg_info json information
"""
working_set = working_set or default_working_set
return _flatten_extras_json(
pkg_names, find_packages_requirements_dists, working_set)
def flatten_parents_extras_json(pkg_names, working_set=None):
"""
Traverses through the dependency graph of packages 'pkg_names'
and flattens all the egg_info json information for parents of
the specified packages.
"""
working_set = working_set or default_working_set
return _flatten_extras_json(
pkg_names, find_packages_parents_requirements_dists, working_set)
write_extras_json = partial(write_json_file, json_field)
return (
get_extras_json,
flatten_extras_json,
flatten_parents_extras_json,
write_extras_json,
) | [
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calmjs/calmjs | src/calmjs/dist.py | build_helpers_module_registry_dependencies | def build_helpers_module_registry_dependencies(registry_name='calmjs.module'):
"""
Return a tuple of funtions that will provide the functions that
return the relevant sets of module registry records based on the
dependencies defined for the provided packages.
"""
def get_module_registry_dependencies(
pkg_names, registry_name=registry_name, working_set=None):
"""
Get dependencies for the given package names from module
registry identified by registry name.
For the given packages 'pkg_names' and the registry identified
by 'registry_name', resolve the exported location for just the
package.
"""
working_set = working_set or default_working_set
registry = get(registry_name)
if not isinstance(registry, BaseModuleRegistry):
return {}
result = {}
for pkg_name in pkg_names:
result.update(registry.get_records_for_package(pkg_name))
return result
def _flatten_module_registry_dependencies(
pkg_names, registry_name, find_dists, working_set):
"""
Flatten dependencies for the given package names from module
registry identified by registry name using the find_dists
function on the given working_set.
For the given packages 'pkg_names' and the registry identified
by 'registry_name', resolve and flatten all the exported
locations.
"""
result = {}
registry = get(registry_name)
if not isinstance(registry, BaseModuleRegistry):
return result
dists = find_dists(pkg_names, working_set=working_set)
for dist in dists:
result.update(registry.get_records_for_package(dist.project_name))
return result
def flatten_module_registry_dependencies(
pkg_names, registry_name=registry_name, working_set=None):
"""
Flatten dependencies for the specified packages from the module
registry identified by registry name.
For the given packages 'pkg_names' and the registry identified
by 'registry_name', resolve and flatten all the exported
locations.
"""
working_set = working_set or default_working_set
return _flatten_module_registry_dependencies(
pkg_names, registry_name, find_packages_requirements_dists,
working_set)
def flatten_parents_module_registry_dependencies(
pkg_names, registry_name=registry_name, working_set=None):
"""
Flatten dependencies for the parents of the specified packages
from the module registry identified by registry name.
For the given packages 'pkg_names' and the registry identified
by 'registry_name', resolve and flatten all the exported
locations.
"""
working_set = working_set or default_working_set
return _flatten_module_registry_dependencies(
pkg_names, registry_name, find_packages_parents_requirements_dists,
working_set)
return (
get_module_registry_dependencies,
flatten_module_registry_dependencies,
flatten_parents_module_registry_dependencies,
) | python | def build_helpers_module_registry_dependencies(registry_name='calmjs.module'):
"""
Return a tuple of funtions that will provide the functions that
return the relevant sets of module registry records based on the
dependencies defined for the provided packages.
"""
def get_module_registry_dependencies(
pkg_names, registry_name=registry_name, working_set=None):
"""
Get dependencies for the given package names from module
registry identified by registry name.
For the given packages 'pkg_names' and the registry identified
by 'registry_name', resolve the exported location for just the
package.
"""
working_set = working_set or default_working_set
registry = get(registry_name)
if not isinstance(registry, BaseModuleRegistry):
return {}
result = {}
for pkg_name in pkg_names:
result.update(registry.get_records_for_package(pkg_name))
return result
def _flatten_module_registry_dependencies(
pkg_names, registry_name, find_dists, working_set):
"""
Flatten dependencies for the given package names from module
registry identified by registry name using the find_dists
function on the given working_set.
For the given packages 'pkg_names' and the registry identified
by 'registry_name', resolve and flatten all the exported
locations.
"""
result = {}
registry = get(registry_name)
if not isinstance(registry, BaseModuleRegistry):
return result
dists = find_dists(pkg_names, working_set=working_set)
for dist in dists:
result.update(registry.get_records_for_package(dist.project_name))
return result
def flatten_module_registry_dependencies(
pkg_names, registry_name=registry_name, working_set=None):
"""
Flatten dependencies for the specified packages from the module
registry identified by registry name.
For the given packages 'pkg_names' and the registry identified
by 'registry_name', resolve and flatten all the exported
locations.
"""
working_set = working_set or default_working_set
return _flatten_module_registry_dependencies(
pkg_names, registry_name, find_packages_requirements_dists,
working_set)
def flatten_parents_module_registry_dependencies(
pkg_names, registry_name=registry_name, working_set=None):
"""
Flatten dependencies for the parents of the specified packages
from the module registry identified by registry name.
For the given packages 'pkg_names' and the registry identified
by 'registry_name', resolve and flatten all the exported
locations.
"""
working_set = working_set or default_working_set
return _flatten_module_registry_dependencies(
pkg_names, registry_name, find_packages_parents_requirements_dists,
working_set)
return (
get_module_registry_dependencies,
flatten_module_registry_dependencies,
flatten_parents_module_registry_dependencies,
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calmjs/calmjs | src/calmjs/dist.py | has_calmjs_artifact_declarations | def has_calmjs_artifact_declarations(cmd, registry_name='calmjs.artifacts'):
"""
For a distutils command to verify that the artifact build step is
possible.
"""
return any(get(registry_name).iter_records_for(
cmd.distribution.get_name())) | python | def has_calmjs_artifact_declarations(cmd, registry_name='calmjs.artifacts'):
"""
For a distutils command to verify that the artifact build step is
possible.
"""
return any(get(registry_name).iter_records_for(
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calmjs/calmjs | src/calmjs/dist.py | build_calmjs_artifacts | def build_calmjs_artifacts(dist, key, value, cmdclass=BuildCommand):
"""
Trigger the artifact build process through the setuptools.
"""
if value is not True:
return
build_cmd = dist.get_command_obj('build')
if not isinstance(build_cmd, cmdclass):
logger.error(
"'build' command in Distribution is not an instance of "
"'%s:%s' (got %r instead)",
cmdclass.__module__, cmdclass.__name__, build_cmd)
return
build_cmd.sub_commands.append((key, has_calmjs_artifact_declarations)) | python | def build_calmjs_artifacts(dist, key, value, cmdclass=BuildCommand):
"""
Trigger the artifact build process through the setuptools.
"""
if value is not True:
return
build_cmd = dist.get_command_obj('build')
if not isinstance(build_cmd, cmdclass):
logger.error(
"'build' command in Distribution is not an instance of "
"'%s:%s' (got %r instead)",
cmdclass.__module__, cmdclass.__name__, build_cmd)
return
build_cmd.sub_commands.append((key, has_calmjs_artifact_declarations)) | [
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weso/CWR-DataApi | cwr/grammar/factory/rule.py | FieldRuleFactory.get_rule | def get_rule(self, field_id):
"""
Returns the rule for the field identified by the id.
If it is set as not being compulsory, the rule will be adapted to
accept string composed only of white characters.
:param field_id: unique id in the system for the field
:return: the rule of a field
"""
if field_id in self._fields:
# Field already exists
field = self._fields[field_id]
else:
# Field does not exist
# It is created
field = self._create_field(field_id)
# Field is saved
self._fields[field_id] = field
return field | python | def get_rule(self, field_id):
"""
Returns the rule for the field identified by the id.
If it is set as not being compulsory, the rule will be adapted to
accept string composed only of white characters.
:param field_id: unique id in the system for the field
:return: the rule of a field
"""
if field_id in self._fields:
# Field already exists
field = self._fields[field_id]
else:
# Field does not exist
# It is created
field = self._create_field(field_id)
# Field is saved
self._fields[field_id] = field
return field | [
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weso/CWR-DataApi | cwr/grammar/factory/rule.py | FieldRuleFactory._create_field | def _create_field(self, field_id):
"""
Creates the field with the specified parameters.
:param field_id: identifier for the field
:return: the basic rule for the field
"""
# Field configuration info
config = self._field_configs[field_id]
adapter = self._adapters[config['type']]
if 'name' in config:
name = config['name']
else:
name = None
if 'size' in config:
columns = config['size']
else:
columns = None
if 'values' in config:
values = config['values']
else:
values = None
field = adapter.get_field(name, columns, values)
if 'results_name' in config:
field = field.setResultsName(config['results_name'])
else:
field = field.setResultsName(field_id)
return field | python | def _create_field(self, field_id):
"""
Creates the field with the specified parameters.
:param field_id: identifier for the field
:return: the basic rule for the field
"""
# Field configuration info
config = self._field_configs[field_id]
adapter = self._adapters[config['type']]
if 'name' in config:
name = config['name']
else:
name = None
if 'size' in config:
columns = config['size']
else:
columns = None
if 'values' in config:
values = config['values']
else:
values = None
field = adapter.get_field(name, columns, values)
if 'results_name' in config:
field = field.setResultsName(config['results_name'])
else:
field = field.setResultsName(field_id)
return field | [
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weso/CWR-DataApi | data_cwr/accessor.py | _FileReader.read_csv_file | def read_csv_file(self, file_name):
"""
Parses a CSV file into a list.
:param file_name: name of the CSV file
:return: a list with the file's contents
"""
result = []
with open(os.path.join(self.__path(), os.path.basename(file_name)),
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headers_reader = csv.reader(csvfile, delimiter=',', quotechar='|')
for type_row in headers_reader:
for t in type_row:
result.append(t)
return result | python | def read_csv_file(self, file_name):
"""
Parses a CSV file into a list.
:param file_name: name of the CSV file
:return: a list with the file's contents
"""
result = []
with open(os.path.join(self.__path(), os.path.basename(file_name)),
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headers_reader = csv.reader(csvfile, delimiter=',', quotechar='|')
for type_row in headers_reader:
for t in type_row:
result.append(t)
return result | [
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weso/CWR-DataApi | data_cwr/accessor.py | _FileReader.read_yaml_file | def read_yaml_file(self, file_name):
"""
Parses a YAML file into a matrix.
:param file_name: name of the YAML file
:return: a matrix with the file's contents
"""
with open(os.path.join(self.__path(), os.path.basename(file_name)),
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return yaml.load(yamlfile) | python | def read_yaml_file(self, file_name):
"""
Parses a YAML file into a matrix.
:param file_name: name of the YAML file
:return: a matrix with the file's contents
"""
with open(os.path.join(self.__path(), os.path.basename(file_name)),
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weso/CWR-DataApi | data_cwr/accessor.py | CWRTables.get_data | def get_data(self, file_id):
"""
Acquires the data from the table identified by the id.
The file is read only once, consecutive calls to this method will
return the sale collection.
:param file_id: identifier for the table
:return: all the values from the table
"""
if file_id not in self._file_values:
file_contents = 'cwr_%s.csv' % file_id
self._file_values[file_id] = self._reader.read_csv_file(
file_contents)
return self._file_values[file_id] | python | def get_data(self, file_id):
"""
Acquires the data from the table identified by the id.
The file is read only once, consecutive calls to this method will
return the sale collection.
:param file_id: identifier for the table
:return: all the values from the table
"""
if file_id not in self._file_values:
file_contents = 'cwr_%s.csv' % file_id
self._file_values[file_id] = self._reader.read_csv_file(
file_contents)
return self._file_values[file_id] | [
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weso/CWR-DataApi | cwr/grammar/field/record.py | record_type | def record_type(values):
"""
Creates a record type field.
These serve as the header field on records, identifying them.
Usually this field can be only an specific value, but sometimes a small
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:param values: allowed record type codes
:return: grammar for the record type field
"""
field = basic.lookup(values, name='Record Type (one of %s)' % values)
return field.setResultsName('record_type') | python | def record_type(values):
"""
Creates a record type field.
These serve as the header field on records, identifying them.
Usually this field can be only an specific value, but sometimes a small
range of codes is allowed. This is specified by the 'values' parameter.
While it is possible to set this field as optional, it is expected to be
compulsory.
:param values: allowed record type codes
:return: grammar for the record type field
"""
field = basic.lookup(values, name='Record Type (one of %s)' % values)
return field.setResultsName('record_type') | [
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weso/CWR-DataApi | cwr/grammar/field/record.py | record_prefix | def record_prefix(required_type, factory):
"""
Creates a record prefix for the specified record type.
:param required_type: the type of the record using this prefix
:param factory: field factory
:return: the record prefix
"""
field = record_type(required_type)
field += factory.get_rule('transaction_sequence_n')
field += factory.get_rule('record_sequence_n')
# field.leaveWhitespace()
return field | python | def record_prefix(required_type, factory):
"""
Creates a record prefix for the specified record type.
:param required_type: the type of the record using this prefix
:param factory: field factory
:return: the record prefix
"""
field = record_type(required_type)
field += factory.get_rule('transaction_sequence_n')
field += factory.get_rule('record_sequence_n')
# field.leaveWhitespace()
return field | [
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weso/CWR-DataApi | config_cwr/accessor.py | _FileReader.read_config_file | def read_config_file(self, file_name):
"""
Reads a CWR grammar config file.
:param file_name: name of the text file
:return: the file's contents
"""
with open(os.path.join(self.__path(), os.path.basename(file_name)),
'rt') as file_config:
return self._parser.parseString(file_config.read()) | python | def read_config_file(self, file_name):
"""
Reads a CWR grammar config file.
:param file_name: name of the text file
:return: the file's contents
"""
with open(os.path.join(self.__path(), os.path.basename(file_name)),
'rt') as file_config:
return self._parser.parseString(file_config.read()) | [
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weso/CWR-DataApi | config_cwr/accessor.py | CWRConfiguration._load_cwr_defaults | def _load_cwr_defaults(self):
"""
Loads the CWR default values file, creating a matrix from it, and then
returns this data.
The file will only be loaded once.
:return: the CWR default values matrix
"""
if self._cwr_defaults is None:
self._cwr_defaults = self._reader.read_yaml_file(
self._file_defaults)
return self._cwr_defaults | python | def _load_cwr_defaults(self):
"""
Loads the CWR default values file, creating a matrix from it, and then
returns this data.
The file will only be loaded once.
:return: the CWR default values matrix
"""
if self._cwr_defaults is None:
self._cwr_defaults = self._reader.read_yaml_file(
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return self._cwr_defaults | [
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calmjs/calmjs | src/calmjs/argparse.py | ArgumentParser.soft_error | def soft_error(self, message):
"""
Same as error, without the dying in a fire part.
"""
self.print_usage(sys.stderr)
args = {'prog': self.prog, 'message': message}
self._print_message(
_('%(prog)s: error: %(message)s\n') % args, sys.stderr) | python | def soft_error(self, message):
"""
Same as error, without the dying in a fire part.
"""
self.print_usage(sys.stderr)
args = {'prog': self.prog, 'message': message}
self._print_message(
_('%(prog)s: error: %(message)s\n') % args, sys.stderr) | [
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weso/CWR-DataApi | cwr/parser/decoder/file.py | default_filename_decoder | def default_filename_decoder():
"""
Creates a decoder which parses CWR filenames following the old or the new
convention.
:return: a CWR filename decoder for the old and the new conventions
"""
factory = default_filename_grammar_factory()
grammar_old = factory.get_rule('filename_old')
grammar_new = factory.get_rule('filename_new')
return FileNameDecoder(grammar_old, grammar_new) | python | def default_filename_decoder():
"""
Creates a decoder which parses CWR filenames following the old or the new
convention.
:return: a CWR filename decoder for the old and the new conventions
"""
factory = default_filename_grammar_factory()
grammar_old = factory.get_rule('filename_old')
grammar_new = factory.get_rule('filename_new')
return FileNameDecoder(grammar_old, grammar_new) | [
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weso/CWR-DataApi | cwr/parser/decoder/file.py | FileDecoder.decode | def decode(self, data):
"""
Parses the file, creating a CWRFile from it.
It requires a dictionary with two values:
- filename, containing the filename
- contents, containing the file contents
:param data: dictionary with the data to parse
:return: a CWRFile instance
"""
file_name = self._filename_decoder.decode(data['filename'])
file_data = data['contents']
i = 0
max_size = len(file_data)
while file_data[i:i + 1] != 'H' and i < max_size:
i += 1
if i > 0:
data['contents'] = file_data[i:]
transmission = self._file_decoder.decode(data['contents'])[0]
return CWRFile(file_name, transmission) | python | def decode(self, data):
"""
Parses the file, creating a CWRFile from it.
It requires a dictionary with two values:
- filename, containing the filename
- contents, containing the file contents
:param data: dictionary with the data to parse
:return: a CWRFile instance
"""
file_name = self._filename_decoder.decode(data['filename'])
file_data = data['contents']
i = 0
max_size = len(file_data)
while file_data[i:i + 1] != 'H' and i < max_size:
i += 1
if i > 0:
data['contents'] = file_data[i:]
transmission = self._file_decoder.decode(data['contents'])[0]
return CWRFile(file_name, transmission) | [
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weso/CWR-DataApi | cwr/parser/decoder/file.py | FileNameDecoder.decode | def decode(self, file_name):
"""
Parses the filename, creating a FileTag from it.
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not conform any of them, then an empty FileTag will be returned.
:param file_name: filename to parse
:return: a FileTag instance
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try:
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except:
try:
file_tag = self._filename_decoder_old.decode(file_name)
except:
file_tag = FileTag(0, 0, '', '', '')
return file_tag | python | def decode(self, file_name):
"""
Parses the filename, creating a FileTag from it.
It will try both the old and the new conventions, if the filename does
not conform any of them, then an empty FileTag will be returned.
:param file_name: filename to parse
:return: a FileTag instance
"""
try:
file_tag = self._filename_decoder_new.decode(file_name)
except:
try:
file_tag = self._filename_decoder_old.decode(file_name)
except:
file_tag = FileTag(0, 0, '', '', '')
return file_tag | [
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calmjs/calmjs | src/calmjs/utils.py | enable_pretty_logging | def enable_pretty_logging(logger='calmjs', level=logging.DEBUG, stream=None):
"""
Shorthand to enable pretty logging
"""
def cleanup():
logger.removeHandler(handler)
logger.level = old_level
if not isinstance(logger, logging.Logger):
logger = logging.getLogger(logger)
old_level = logger.level
handler = logging.StreamHandler(stream)
handler.setFormatter(logging.Formatter(
u'%(asctime)s %(levelname)s %(name)s %(message)s'))
logger.addHandler(handler)
logger.setLevel(level)
return cleanup | python | def enable_pretty_logging(logger='calmjs', level=logging.DEBUG, stream=None):
"""
Shorthand to enable pretty logging
"""
def cleanup():
logger.removeHandler(handler)
logger.level = old_level
if not isinstance(logger, logging.Logger):
logger = logging.getLogger(logger)
old_level = logger.level
handler = logging.StreamHandler(stream)
handler.setFormatter(logging.Formatter(
u'%(asctime)s %(levelname)s %(name)s %(message)s'))
logger.addHandler(handler)
logger.setLevel(level)
return cleanup | [
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calmjs/calmjs | src/calmjs/utils.py | finalize_env | def finalize_env(env):
"""
Produce a platform specific env for passing into subprocess.Popen
family of external process calling methods, and the supplied env
will be updated on top of it. Returns a new env.
"""
keys = _PLATFORM_ENV_KEYS.get(sys.platform, [])
if 'PATH' not in keys:
# this MUST be available due to Node.js (and others really)
# needing something to look for binary locations when it shells
# out to other binaries.
keys.append('PATH')
results = {
key: os.environ.get(key, '') for key in keys
}
results.update(env)
return results | python | def finalize_env(env):
"""
Produce a platform specific env for passing into subprocess.Popen
family of external process calling methods, and the supplied env
will be updated on top of it. Returns a new env.
"""
keys = _PLATFORM_ENV_KEYS.get(sys.platform, [])
if 'PATH' not in keys:
# this MUST be available due to Node.js (and others really)
# needing something to look for binary locations when it shells
# out to other binaries.
keys.append('PATH')
results = {
key: os.environ.get(key, '') for key in keys
}
results.update(env)
return results | [
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calmjs/calmjs | src/calmjs/utils.py | fork_exec | def fork_exec(args, stdin='', **kwargs):
"""
Do a fork-exec through the subprocess.Popen abstraction in a way
that takes a stdin and return stdout.
"""
as_bytes = isinstance(stdin, bytes)
source = stdin if as_bytes else stdin.encode(locale)
p = Popen(args, stdin=PIPE, stdout=PIPE, stderr=PIPE, **kwargs)
stdout, stderr = p.communicate(source)
if as_bytes:
return stdout, stderr
return (stdout.decode(locale), stderr.decode(locale)) | python | def fork_exec(args, stdin='', **kwargs):
"""
Do a fork-exec through the subprocess.Popen abstraction in a way
that takes a stdin and return stdout.
"""
as_bytes = isinstance(stdin, bytes)
source = stdin if as_bytes else stdin.encode(locale)
p = Popen(args, stdin=PIPE, stdout=PIPE, stderr=PIPE, **kwargs)
stdout, stderr = p.communicate(source)
if as_bytes:
return stdout, stderr
return (stdout.decode(locale), stderr.decode(locale)) | [
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calmjs/calmjs | src/calmjs/utils.py | raise_os_error | def raise_os_error(_errno, path=None):
"""
Helper for raising the correct exception under Python 3 while still
being able to raise the same common exception class in Python 2.7.
"""
msg = "%s: '%s'" % (strerror(_errno), path) if path else strerror(_errno)
raise OSError(_errno, msg) | python | def raise_os_error(_errno, path=None):
"""
Helper for raising the correct exception under Python 3 while still
being able to raise the same common exception class in Python 2.7.
"""
msg = "%s: '%s'" % (strerror(_errno), path) if path else strerror(_errno)
raise OSError(_errno, msg) | [
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calmjs/calmjs | src/calmjs/utils.py | which | def which(cmd, mode=os.F_OK | os.X_OK, path=None):
"""
Given cmd, check where it is on PATH.
Loosely based on the version in python 3.3.
"""
if os.path.dirname(cmd):
if os.path.isfile(cmd) and os.access(cmd, mode):
return cmd
if path is None:
path = os.environ.get('PATH', defpath)
if not path:
return None
paths = path.split(pathsep)
if sys.platform == 'win32':
# oh boy
if curdir not in paths:
paths = [curdir] + paths
# also need to check the fileexts...
pathext = os.environ.get('PATHEXT', '').split(pathsep)
if any(cmd.lower().endswith(ext.lower()) for ext in pathext):
files = [cmd]
else:
files = [cmd + ext for ext in pathext]
else:
# sanity
files = [cmd]
seen = set()
for p in paths:
normpath = normcase(p)
if normpath in seen:
continue
seen.add(normpath)
for f in files:
fn = os.path.join(p, f)
if os.path.isfile(fn) and os.access(fn, mode):
return fn
return None | python | def which(cmd, mode=os.F_OK | os.X_OK, path=None):
"""
Given cmd, check where it is on PATH.
Loosely based on the version in python 3.3.
"""
if os.path.dirname(cmd):
if os.path.isfile(cmd) and os.access(cmd, mode):
return cmd
if path is None:
path = os.environ.get('PATH', defpath)
if not path:
return None
paths = path.split(pathsep)
if sys.platform == 'win32':
# oh boy
if curdir not in paths:
paths = [curdir] + paths
# also need to check the fileexts...
pathext = os.environ.get('PATHEXT', '').split(pathsep)
if any(cmd.lower().endswith(ext.lower()) for ext in pathext):
files = [cmd]
else:
files = [cmd + ext for ext in pathext]
else:
# sanity
files = [cmd]
seen = set()
for p in paths:
normpath = normcase(p)
if normpath in seen:
continue
seen.add(normpath)
for f in files:
fn = os.path.join(p, f)
if os.path.isfile(fn) and os.access(fn, mode):
return fn
return None | [
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calmjs/calmjs | src/calmjs/registry.py | Registry._init | def _init(self):
"""
Turn the records into actual usable keys.
"""
self._entry_points = {}
for entry_point in self.raw_entry_points:
if entry_point.dist.project_name != self.reserved.get(
entry_point.name, entry_point.dist.project_name):
logger.error(
"registry '%s' for '%s' is reserved for package '%s'",
entry_point.name, self.registry_name,
self.reserved[entry_point.name],
)
continue
if self.get_record(entry_point.name):
logger.warning(
"registry '%s' for '%s' is already registered.",
entry_point.name, self.registry_name,
)
existing = self._entry_points[entry_point.name]
logger.debug(
"registered '%s' from '%s'", existing, existing.dist)
logger.debug(
"discarded '%s' from '%s'", entry_point, entry_point.dist)
continue
logger.debug(
"recording '%s' from '%s'", entry_point, entry_point.dist)
self._entry_points[entry_point.name] = entry_point | python | def _init(self):
"""
Turn the records into actual usable keys.
"""
self._entry_points = {}
for entry_point in self.raw_entry_points:
if entry_point.dist.project_name != self.reserved.get(
entry_point.name, entry_point.dist.project_name):
logger.error(
"registry '%s' for '%s' is reserved for package '%s'",
entry_point.name, self.registry_name,
self.reserved[entry_point.name],
)
continue
if self.get_record(entry_point.name):
logger.warning(
"registry '%s' for '%s' is already registered.",
entry_point.name, self.registry_name,
)
existing = self._entry_points[entry_point.name]
logger.debug(
"registered '%s' from '%s'", existing, existing.dist)
logger.debug(
"discarded '%s' from '%s'", entry_point, entry_point.dist)
continue
logger.debug(
"recording '%s' from '%s'", entry_point, entry_point.dist)
self._entry_points[entry_point.name] = entry_point | [
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calmjs/calmjs | src/calmjs/toolchain.py | toolchain_spec_compile_entries | def toolchain_spec_compile_entries(
toolchain, spec, entries, process_name, overwrite_log=None):
"""
The standardized Toolchain Spec Entries compile function
This function accepts a toolchain instance, the spec to be operated
with and the entries provided for the process name. The standard
flow is to deferr the actual processing to the toolchain method
`compile_{process_name}_entry` for each entry in the entries list.
The generic compile entries method for the compile process.
Arguments:
toolchain
The toolchain to be used for the operation.
spec
The spec to be operated with.
entries
The entries for the source.
process_name
The name of the specific compile process of the provided
toolchain.
overwrite_log
A callable that will accept a 4-tuple of suffix, key, original
and new value, if monitoring of overwritten values are required.
suffix is derived from the modpath_suffix or targetpath_suffix
of the toolchain instance, key is the key on any of the keys on
either of those mappings, original and new are the original and
the replacement value.
"""
processor = getattr(toolchain, 'compile_%s_entry' % process_name)
modpath_logger = (
partial(overwrite_log, toolchain.modpath_suffix)
if callable(overwrite_log) else None)
targetpath_logger = (
partial(overwrite_log, toolchain.targetpath_suffix)
if callable(overwrite_log) else None)
return process_compile_entries(
processor, spec, entries, modpath_logger, targetpath_logger) | python | def toolchain_spec_compile_entries(
toolchain, spec, entries, process_name, overwrite_log=None):
"""
The standardized Toolchain Spec Entries compile function
This function accepts a toolchain instance, the spec to be operated
with and the entries provided for the process name. The standard
flow is to deferr the actual processing to the toolchain method
`compile_{process_name}_entry` for each entry in the entries list.
The generic compile entries method for the compile process.
Arguments:
toolchain
The toolchain to be used for the operation.
spec
The spec to be operated with.
entries
The entries for the source.
process_name
The name of the specific compile process of the provided
toolchain.
overwrite_log
A callable that will accept a 4-tuple of suffix, key, original
and new value, if monitoring of overwritten values are required.
suffix is derived from the modpath_suffix or targetpath_suffix
of the toolchain instance, key is the key on any of the keys on
either of those mappings, original and new are the original and
the replacement value.
"""
processor = getattr(toolchain, 'compile_%s_entry' % process_name)
modpath_logger = (
partial(overwrite_log, toolchain.modpath_suffix)
if callable(overwrite_log) else None)
targetpath_logger = (
partial(overwrite_log, toolchain.targetpath_suffix)
if callable(overwrite_log) else None)
return process_compile_entries(
processor, spec, entries, modpath_logger, targetpath_logger) | [
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The spec to be operated with.
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calmjs/calmjs | src/calmjs/toolchain.py | process_compile_entries | def process_compile_entries(
processor, spec, entries, modpath_logger=None, targetpath_logger=None):
"""
The generalized raw spec entry process invocation loop.
"""
# Contains a mapping of the module name to the compiled file's
# relative path starting from the base build_dir.
all_modpaths = {}
all_targets = {}
# List of exported module names, should be equal to all keys of
# the compiled and bundled sources.
all_export_module_names = []
def update(base, fresh, logger):
if callable(logger):
for dupes in dict_update_overwrite_check(base, fresh):
logger(*dupes)
else:
base.update(fresh)
for entry in entries:
modpaths, targetpaths, export_module_names = processor(spec, entry)
update(all_modpaths, modpaths, modpath_logger)
update(all_targets, targetpaths, targetpath_logger)
all_export_module_names.extend(export_module_names)
return all_modpaths, all_targets, all_export_module_names | python | def process_compile_entries(
processor, spec, entries, modpath_logger=None, targetpath_logger=None):
"""
The generalized raw spec entry process invocation loop.
"""
# Contains a mapping of the module name to the compiled file's
# relative path starting from the base build_dir.
all_modpaths = {}
all_targets = {}
# List of exported module names, should be equal to all keys of
# the compiled and bundled sources.
all_export_module_names = []
def update(base, fresh, logger):
if callable(logger):
for dupes in dict_update_overwrite_check(base, fresh):
logger(*dupes)
else:
base.update(fresh)
for entry in entries:
modpaths, targetpaths, export_module_names = processor(spec, entry)
update(all_modpaths, modpaths, modpath_logger)
update(all_targets, targetpaths, targetpath_logger)
all_export_module_names.extend(export_module_names)
return all_modpaths, all_targets, all_export_module_names | [
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calmjs/calmjs | src/calmjs/toolchain.py | Spec.update_selected | def update_selected(self, other, selected):
"""
Like update, however a list of selected keys must be provided.
"""
self.update({k: other[k] for k in selected}) | python | def update_selected(self, other, selected):
"""
Like update, however a list of selected keys must be provided.
"""
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calmjs/calmjs | src/calmjs/toolchain.py | Spec.advise | def advise(self, name, f, *a, **kw):
"""
Add an advice that will be handled later by the handle method.
Arguments:
name
The name of the advice group
f
A callable method or function.
The rest of the arguments will be passed as arguments and
keyword arguments to f when it's invoked.
"""
if name is None:
return
advice = (f, a, kw)
debug = self.get(DEBUG)
frame = currentframe()
if frame is None:
logger.debug('currentframe() failed to return frame')
else:
if name in self._called:
self.__advice_stack_frame_protection(frame)
if debug:
logger.debug(
"advise '%s' invoked by %s:%d",
name,
frame.f_back.f_code.co_filename, frame.f_back.f_lineno,
)
if debug > 1:
# use the memory address of the tuple which should
# be stable
self._frames[id(advice)] = ''.join(
format_stack(frame.f_back))
self._advices[name] = self._advices.get(name, [])
self._advices[name].append(advice) | python | def advise(self, name, f, *a, **kw):
"""
Add an advice that will be handled later by the handle method.
Arguments:
name
The name of the advice group
f
A callable method or function.
The rest of the arguments will be passed as arguments and
keyword arguments to f when it's invoked.
"""
if name is None:
return
advice = (f, a, kw)
debug = self.get(DEBUG)
frame = currentframe()
if frame is None:
logger.debug('currentframe() failed to return frame')
else:
if name in self._called:
self.__advice_stack_frame_protection(frame)
if debug:
logger.debug(
"advise '%s' invoked by %s:%d",
name,
frame.f_back.f_code.co_filename, frame.f_back.f_lineno,
)
if debug > 1:
# use the memory address of the tuple which should
# be stable
self._frames[id(advice)] = ''.join(
format_stack(frame.f_back))
self._advices[name] = self._advices.get(name, [])
self._advices[name].append(advice) | [
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The name of the advice group
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A callable method or function.
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calmjs/calmjs | src/calmjs/toolchain.py | Spec.handle | def handle(self, name):
"""
Call all advices at the provided name.
This has an analogue in the join point in aspected oriented
programming, but the analogy is a weak one as we don't have the
proper metaobject protocol to support this. Implementation that
make use of this system should make it clear that they will call
this method with name associated with its group before and after
its execution, or that the method at hand that want this invoked
be called by this other conductor method.
For the Toolchain standard steps (prepare, compile, assemble,
link and finalize), this handle method will only be called by
invoking the toolchain as a callable. Calling those methods
piecemeal will not trigger the invocation, even though it
probably should. Modules, classes and methods that desire to
call their own handler should instead follow the convention
where the handle be called before and after with the appropriate
names. For instance:
def test(self, spec):
spec.handle(BEFORE_TEST)
# do the things
spec.handle(AFTER_TEST)
This arrangement will need to be revisited when a proper system
is written at the metaclass level.
Arguments:
name
The name of the advices group. All the callables
registered to this group will be invoked, last-in-first-out.
"""
if name in self._called:
logger.warning(
"advice group '%s' has been called for this spec %r",
name, self,
)
# only now ensure checking
self.__advice_stack_frame_protection(currentframe())
else:
self._called.add(name)
# Get a complete clone, so indirect manipulation done to the
# reference that others have access to will not have an effect
# within the scope of this execution. Please refer to the
# test_toolchain, test_spec_advice_no_infinite_pop test case.
advices = []
advices.extend(self._advices.get(name, []))
if advices and self.get('debug'):
logger.debug(
"handling %d advices in group '%s' ", len(advices), name)
while advices:
try:
# cleanup basically done lifo (last in first out)
values = advices.pop()
advice, a, kw = values
if not ((callable(advice)) and
isinstance(a, tuple) and
isinstance(kw, dict)):
raise TypeError
except ValueError:
logger.info('Spec advice extraction error: got %s', values)
except TypeError:
logger.info('Spec advice malformed: got %s', values)
else:
try:
try:
advice(*a, **kw)
except Exception as e:
# get that back by the id.
frame = self._frames.get(id(values))
if frame:
logger.info('Spec advice exception: %r', e)
logger.info(
'Traceback for original advice:\n%s', frame)
# continue on for the normal exception
raise
except AdviceCancel as e:
logger.info(
"advice %s in group '%s' signaled its cancellation "
"during its execution: %s", advice, name, e
)
if self.get(DEBUG):
logger.debug(
'showing traceback for cancellation', exc_info=1,
)
except AdviceAbort as e:
# this is a signaled error with a planned abortion
logger.warning(
"advice %s in group '%s' encountered a known error "
"during its execution: %s; continuing with toolchain "
"execution", advice, name, e
)
if self.get(DEBUG):
logger.warning(
'showing traceback for error', exc_info=1,
)
except ToolchainCancel:
# this is the safe cancel
raise
except ToolchainAbort as e:
logger.critical(
"an advice in group '%s' triggered an abort: %s",
name, str(e)
)
raise
except KeyboardInterrupt:
raise ToolchainCancel('interrupted')
except Exception as e:
# a completely unplanned failure
logger.critical(
"advice %s in group '%s' terminated due to an "
"unexpected exception: %s", advice, name, e
)
if self.get(DEBUG):
logger.critical(
'showing traceback for error', exc_info=1,
) | python | def handle(self, name):
"""
Call all advices at the provided name.
This has an analogue in the join point in aspected oriented
programming, but the analogy is a weak one as we don't have the
proper metaobject protocol to support this. Implementation that
make use of this system should make it clear that they will call
this method with name associated with its group before and after
its execution, or that the method at hand that want this invoked
be called by this other conductor method.
For the Toolchain standard steps (prepare, compile, assemble,
link and finalize), this handle method will only be called by
invoking the toolchain as a callable. Calling those methods
piecemeal will not trigger the invocation, even though it
probably should. Modules, classes and methods that desire to
call their own handler should instead follow the convention
where the handle be called before and after with the appropriate
names. For instance:
def test(self, spec):
spec.handle(BEFORE_TEST)
# do the things
spec.handle(AFTER_TEST)
This arrangement will need to be revisited when a proper system
is written at the metaclass level.
Arguments:
name
The name of the advices group. All the callables
registered to this group will be invoked, last-in-first-out.
"""
if name in self._called:
logger.warning(
"advice group '%s' has been called for this spec %r",
name, self,
)
# only now ensure checking
self.__advice_stack_frame_protection(currentframe())
else:
self._called.add(name)
# Get a complete clone, so indirect manipulation done to the
# reference that others have access to will not have an effect
# within the scope of this execution. Please refer to the
# test_toolchain, test_spec_advice_no_infinite_pop test case.
advices = []
advices.extend(self._advices.get(name, []))
if advices and self.get('debug'):
logger.debug(
"handling %d advices in group '%s' ", len(advices), name)
while advices:
try:
# cleanup basically done lifo (last in first out)
values = advices.pop()
advice, a, kw = values
if not ((callable(advice)) and
isinstance(a, tuple) and
isinstance(kw, dict)):
raise TypeError
except ValueError:
logger.info('Spec advice extraction error: got %s', values)
except TypeError:
logger.info('Spec advice malformed: got %s', values)
else:
try:
try:
advice(*a, **kw)
except Exception as e:
# get that back by the id.
frame = self._frames.get(id(values))
if frame:
logger.info('Spec advice exception: %r', e)
logger.info(
'Traceback for original advice:\n%s', frame)
# continue on for the normal exception
raise
except AdviceCancel as e:
logger.info(
"advice %s in group '%s' signaled its cancellation "
"during its execution: %s", advice, name, e
)
if self.get(DEBUG):
logger.debug(
'showing traceback for cancellation', exc_info=1,
)
except AdviceAbort as e:
# this is a signaled error with a planned abortion
logger.warning(
"advice %s in group '%s' encountered a known error "
"during its execution: %s; continuing with toolchain "
"execution", advice, name, e
)
if self.get(DEBUG):
logger.warning(
'showing traceback for error', exc_info=1,
)
except ToolchainCancel:
# this is the safe cancel
raise
except ToolchainAbort as e:
logger.critical(
"an advice in group '%s' triggered an abort: %s",
name, str(e)
)
raise
except KeyboardInterrupt:
raise ToolchainCancel('interrupted')
except Exception as e:
# a completely unplanned failure
logger.critical(
"advice %s in group '%s' terminated due to an "
"unexpected exception: %s", advice, name, e
)
if self.get(DEBUG):
logger.critical(
'showing traceback for error', exc_info=1,
) | [
"def",
"handle",
"(",
"self",
",",
"name",
")",
":",
"if",
"name",
"in",
"self",
".",
"_called",
":",
"logger",
".",
"warning",
"(",
"\"advice group '%s' has been called for this spec %r\"",
",",
"name",
",",
"self",
",",
")",
"# only now ensure checking",
"self... | Call all advices at the provided name.
This has an analogue in the join point in aspected oriented
programming, but the analogy is a weak one as we don't have the
proper metaobject protocol to support this. Implementation that
make use of this system should make it clear that they will call
this method with name associated with its group before and after
its execution, or that the method at hand that want this invoked
be called by this other conductor method.
For the Toolchain standard steps (prepare, compile, assemble,
link and finalize), this handle method will only be called by
invoking the toolchain as a callable. Calling those methods
piecemeal will not trigger the invocation, even though it
probably should. Modules, classes and methods that desire to
call their own handler should instead follow the convention
where the handle be called before and after with the appropriate
names. For instance:
def test(self, spec):
spec.handle(BEFORE_TEST)
# do the things
spec.handle(AFTER_TEST)
This arrangement will need to be revisited when a proper system
is written at the metaclass level.
Arguments:
name
The name of the advices group. All the callables
registered to this group will be invoked, last-in-first-out. | [
"Call",
"all",
"advices",
"at",
"the",
"provided",
"name",
"."
] | b9b407c2b6a7662da64bccba93bb8d92e7a5fafd | https://github.com/calmjs/calmjs/blob/b9b407c2b6a7662da64bccba93bb8d92e7a5fafd/src/calmjs/toolchain.py#L708-L831 | train | 45,799 |
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