repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_code_tokens listlengths 15 672k | func_documentation_string stringlengths 1 47.2k | func_documentation_tokens listlengths 1 3.92k | split_name stringclasses 1
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kejbaly2/metrique | metrique/reporting.py | Report.add_chapter | def add_chapter(self, title):
'''
Adds a new chapter to the report.
:param str title: Title of the chapter.
'''
chap_id = 'chap%s' % self.chap_counter
self.chap_counter += 1
self.sidebar += '<a href="#%s" class="list-group-item">%s</a>\n' % (
chap_id, title)
self.body += '<h1 id="%s">%s</h1>\n' % (chap_id, title) | python | def add_chapter(self, title):
'''
Adds a new chapter to the report.
:param str title: Title of the chapter.
'''
chap_id = 'chap%s' % self.chap_counter
self.chap_counter += 1
self.sidebar += '<a href="#%s" class="list-group-item">%s</a>\n' % (
chap_id, title)
self.body += '<h1 id="%s">%s</h1>\n' % (chap_id, title) | [
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kejbaly2/metrique | metrique/reporting.py | Report.add_image | def add_image(self, figure, dpi=72):
'''
Adds an image to the last chapter/section.
The image will be stored in the `{self.title}_files` directory.
:param matplotlib.figure figure:
A matplotlib figure to be saved into the report
'''
name = os.path.join(self._dir, '/fig%s.png' % self.fig_counter)
self.fig_counter += 1
figure.savefig(name, dpi=dpi)
plt.close(figure)
self.body += '<img src="%s" />\n' % name | python | def add_image(self, figure, dpi=72):
'''
Adds an image to the last chapter/section.
The image will be stored in the `{self.title}_files` directory.
:param matplotlib.figure figure:
A matplotlib figure to be saved into the report
'''
name = os.path.join(self._dir, '/fig%s.png' % self.fig_counter)
self.fig_counter += 1
figure.savefig(name, dpi=dpi)
plt.close(figure)
self.body += '<img src="%s" />\n' % name | [
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kejbaly2/metrique | metrique/reporting.py | Report.write_report | def write_report(self, force=False):
'''
Writes the report to a file.
'''
path = self.title + '.html'
value = self._template.format(
title=self.title, body=self.body, sidebar=self.sidebar)
write_file(path, value, force=force)
plt.ion() | python | def write_report(self, force=False):
'''
Writes the report to a file.
'''
path = self.title + '.html'
value = self._template.format(
title=self.title, body=self.body, sidebar=self.sidebar)
write_file(path, value, force=force)
plt.ion() | [
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biocore/burrito-fillings | bfillings/fasttree_v1.py | build_tree_from_alignment | def build_tree_from_alignment(aln, moltype=DNA, best_tree=False, params=None):
"""Returns a tree from alignment
Will check MolType of aln object
"""
if params is None:
params = {}
if moltype == DNA or moltype == RNA:
params['-nt'] = True
elif moltype == PROTEIN:
params['-nt'] = False
else:
raise ValueError, \
"FastTree does not support moltype: %s" % moltype.label
app = FastTree(params=params)
if best_tree:
raise NotImplementedError, "best_tree not implemented yet"
result = app(aln.toFasta())
tree = DndParser(result['Tree'].read(), constructor=PhyloNode)
return tree | python | def build_tree_from_alignment(aln, moltype=DNA, best_tree=False, params=None):
"""Returns a tree from alignment
Will check MolType of aln object
"""
if params is None:
params = {}
if moltype == DNA or moltype == RNA:
params['-nt'] = True
elif moltype == PROTEIN:
params['-nt'] = False
else:
raise ValueError, \
"FastTree does not support moltype: %s" % moltype.label
app = FastTree(params=params)
if best_tree:
raise NotImplementedError, "best_tree not implemented yet"
result = app(aln.toFasta())
tree = DndParser(result['Tree'].read(), constructor=PhyloNode)
return tree | [
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castelao/oceansdb | oceansdb/utils.py | dbsource | def dbsource(dbname, var, resolution=None, tscale=None):
"""Return which file(s) to use according to dbname, var, etc
"""
db_cfg = {}
cfg_dir = 'datasource'
cfg_files = pkg_resources.resource_listdir('oceansdb', cfg_dir)
cfg_files = [f for f in cfg_files if f[-5:] == '.json']
for src_cfg in cfg_files:
text = pkg_resources.resource_string(
'oceansdb', os.path.join(cfg_dir, src_cfg))
text = text.decode('UTF-8', 'replace')
cfg = json.loads(text)
for c in cfg:
assert c not in db_cfg, "Trying to overwrite %s"
db_cfg[c] = cfg[c]
dbpath = oceansdb_dir()
datafiles = []
cfg = db_cfg[dbname]
if (resolution is None):
resolution = cfg['vars'][var]['default_resolution']
if (tscale is None):
tscale = cfg['vars'][var][resolution]["default_tscale"]
for c in cfg['vars'][var][resolution][tscale]:
download_file(outputdir=dbpath, **c)
if 'filename' in c:
filename = os.path.join(dbpath, c['filename'])
else:
filename = os.path.join(dbpath,
os.path.basename(urlparse(c['url']).path))
if 'varnames' in cfg['vars'][var][resolution]:
datafiles.append(Dataset_flex(filename,
aliases=cfg['vars'][var][resolution]['varnames']))
else:
datafiles.append(Dataset_flex(filename))
return datafiles | python | def dbsource(dbname, var, resolution=None, tscale=None):
"""Return which file(s) to use according to dbname, var, etc
"""
db_cfg = {}
cfg_dir = 'datasource'
cfg_files = pkg_resources.resource_listdir('oceansdb', cfg_dir)
cfg_files = [f for f in cfg_files if f[-5:] == '.json']
for src_cfg in cfg_files:
text = pkg_resources.resource_string(
'oceansdb', os.path.join(cfg_dir, src_cfg))
text = text.decode('UTF-8', 'replace')
cfg = json.loads(text)
for c in cfg:
assert c not in db_cfg, "Trying to overwrite %s"
db_cfg[c] = cfg[c]
dbpath = oceansdb_dir()
datafiles = []
cfg = db_cfg[dbname]
if (resolution is None):
resolution = cfg['vars'][var]['default_resolution']
if (tscale is None):
tscale = cfg['vars'][var][resolution]["default_tscale"]
for c in cfg['vars'][var][resolution][tscale]:
download_file(outputdir=dbpath, **c)
if 'filename' in c:
filename = os.path.join(dbpath, c['filename'])
else:
filename = os.path.join(dbpath,
os.path.basename(urlparse(c['url']).path))
if 'varnames' in cfg['vars'][var][resolution]:
datafiles.append(Dataset_flex(filename,
aliases=cfg['vars'][var][resolution]['varnames']))
else:
datafiles.append(Dataset_flex(filename))
return datafiles | [
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halfak/deltas | deltas/algorithms/sequence_matcher.py | diff | def diff(a, b):
"""
Performs a longest common substring diff.
:Parameters:
a : sequence of `comparable`
Initial sequence
b : sequence of `comparable`
Changed sequence
:Returns:
An `iterable` of operations.
"""
a, b = list(a), list(b)
opcodes = SM(None, a, b).get_opcodes()
return parse_opcodes(opcodes) | python | def diff(a, b):
"""
Performs a longest common substring diff.
:Parameters:
a : sequence of `comparable`
Initial sequence
b : sequence of `comparable`
Changed sequence
:Returns:
An `iterable` of operations.
"""
a, b = list(a), list(b)
opcodes = SM(None, a, b).get_opcodes()
return parse_opcodes(opcodes) | [
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michaelpb/omnic | omnic/conversion/utils.py | convert_endpoint | async def convert_endpoint(url_string, ts, is_just_checking):
'''
Main logic for HTTP endpoint.
'''
response = singletons.server.response
# Prep ForeignResource and ensure does not validate security settings
singletons.settings
foreign_res = ForeignResource(url_string)
target_ts = TypeString(ts)
target_resource = TypedResource(url_string, target_ts)
# Send back cache if it exists
if target_resource.cache_exists():
if is_just_checking:
return _just_checking_response(True, target_resource)
return await response.file(target_resource.cache_path, headers={
'Content-Type': target_ts.mimetype,
})
# Check if already downloaded. If not, queue up download.
if not foreign_res.cache_exists():
singletons.workers.enqueue_download(foreign_res)
# Queue up a single function that will in turn queue up conversion
# process
singletons.workers.enqueue_sync(
enqueue_conversion_path,
url_string,
str(target_ts),
singletons.workers.enqueue_convert
)
if is_just_checking:
return _just_checking_response(False, target_resource)
# Respond with placeholder
return singletons.placeholders.stream_response(target_ts, response) | python | async def convert_endpoint(url_string, ts, is_just_checking):
'''
Main logic for HTTP endpoint.
'''
response = singletons.server.response
# Prep ForeignResource and ensure does not validate security settings
singletons.settings
foreign_res = ForeignResource(url_string)
target_ts = TypeString(ts)
target_resource = TypedResource(url_string, target_ts)
# Send back cache if it exists
if target_resource.cache_exists():
if is_just_checking:
return _just_checking_response(True, target_resource)
return await response.file(target_resource.cache_path, headers={
'Content-Type': target_ts.mimetype,
})
# Check if already downloaded. If not, queue up download.
if not foreign_res.cache_exists():
singletons.workers.enqueue_download(foreign_res)
# Queue up a single function that will in turn queue up conversion
# process
singletons.workers.enqueue_sync(
enqueue_conversion_path,
url_string,
str(target_ts),
singletons.workers.enqueue_convert
)
if is_just_checking:
return _just_checking_response(False, target_resource)
# Respond with placeholder
return singletons.placeholders.stream_response(target_ts, response) | [
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michaelpb/omnic | omnic/conversion/utils.py | apply_command_list_template | def apply_command_list_template(command_list, in_path, out_path, args):
'''
Perform necessary substitutions on a command list to create a CLI-ready
list to launch a conversion or download process via system binary.
'''
replacements = {
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'$OUT': out_path,
}
# Add in positional arguments ($0, $1, etc)
for i, arg in enumerate(args):
replacements['$' + str(i)] = arg
results = [replacements.get(arg, arg) for arg in command_list]
# Returns list of truthy replaced arguments in command
return [item for item in results if item] | python | def apply_command_list_template(command_list, in_path, out_path, args):
'''
Perform necessary substitutions on a command list to create a CLI-ready
list to launch a conversion or download process via system binary.
'''
replacements = {
'$IN': in_path,
'$OUT': out_path,
}
# Add in positional arguments ($0, $1, etc)
for i, arg in enumerate(args):
replacements['$' + str(i)] = arg
results = [replacements.get(arg, arg) for arg in command_list]
# Returns list of truthy replaced arguments in command
return [item for item in results if item] | [
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michaelpb/omnic | omnic/conversion/utils.py | convert_local | async def convert_local(path, to_type):
'''
Given an absolute path to a local file, convert to a given to_type
'''
# Now find path between types
typed_foreign_res = TypedLocalResource(path)
original_ts = typed_foreign_res.typestring
conversion_path = singletons.converter_graph.find_path(
original_ts, to_type)
# print('Conversion path: ', conversion_path)
# Loop through each step in graph path and convert
for is_first, is_last, path_step in first_last_iterator(conversion_path):
converter_class, from_ts, to_ts = path_step
converter = converter_class()
in_resource = TypedLocalResource(path, from_ts)
if is_first: # Ensure first resource is just the source one
in_resource = typed_foreign_res
out_resource = TypedLocalResource(path, to_ts)
if is_last:
out_resource = TypedPathedLocalResource(path, to_ts)
await converter.convert(in_resource, out_resource) | python | async def convert_local(path, to_type):
'''
Given an absolute path to a local file, convert to a given to_type
'''
# Now find path between types
typed_foreign_res = TypedLocalResource(path)
original_ts = typed_foreign_res.typestring
conversion_path = singletons.converter_graph.find_path(
original_ts, to_type)
# print('Conversion path: ', conversion_path)
# Loop through each step in graph path and convert
for is_first, is_last, path_step in first_last_iterator(conversion_path):
converter_class, from_ts, to_ts = path_step
converter = converter_class()
in_resource = TypedLocalResource(path, from_ts)
if is_first: # Ensure first resource is just the source one
in_resource = typed_foreign_res
out_resource = TypedLocalResource(path, to_ts)
if is_last:
out_resource = TypedPathedLocalResource(path, to_ts)
await converter.convert(in_resource, out_resource) | [
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michaelpb/omnic | omnic/conversion/utils.py | enqueue_conversion_path | def enqueue_conversion_path(url_string, to_type, enqueue_convert):
'''
Given a URL string that has already been downloaded, enqueue
necessary conversion to get to target type
'''
target_ts = TypeString(to_type)
foreign_res = ForeignResource(url_string)
# Determine the file type of the foreign resource
typed_foreign_res = foreign_res.guess_typed()
if not typed_foreign_res.cache_exists():
# Symlink to new location that includes typed extension
typed_foreign_res.symlink_from(foreign_res)
# Now find path between types
original_ts = typed_foreign_res.typestring
path = singletons.converter_graph.find_path(original_ts, target_ts)
# Loop through each step in graph path and convert
is_first = True
for converter_class, from_ts, to_ts in path:
converter = converter_class()
in_resource = TypedResource(url_string, from_ts)
if is_first: # Ensure first resource is just the source one
in_resource = TypedForeignResource(url_string, from_ts)
out_resource = TypedResource(url_string, to_ts)
enqueue_convert(converter, in_resource, out_resource)
is_first = False | python | def enqueue_conversion_path(url_string, to_type, enqueue_convert):
'''
Given a URL string that has already been downloaded, enqueue
necessary conversion to get to target type
'''
target_ts = TypeString(to_type)
foreign_res = ForeignResource(url_string)
# Determine the file type of the foreign resource
typed_foreign_res = foreign_res.guess_typed()
if not typed_foreign_res.cache_exists():
# Symlink to new location that includes typed extension
typed_foreign_res.symlink_from(foreign_res)
# Now find path between types
original_ts = typed_foreign_res.typestring
path = singletons.converter_graph.find_path(original_ts, target_ts)
# Loop through each step in graph path and convert
is_first = True
for converter_class, from_ts, to_ts in path:
converter = converter_class()
in_resource = TypedResource(url_string, from_ts)
if is_first: # Ensure first resource is just the source one
in_resource = TypedForeignResource(url_string, from_ts)
out_resource = TypedResource(url_string, to_ts)
enqueue_convert(converter, in_resource, out_resource)
is_first = False | [
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dailymuse/oz | oz/core/actions.py | check_path | def check_path(path, otherwise):
"""
Checks if a path exists. If it does, print a warning message; if not,
execute the `otherwise` callback argument.
"""
if os.path.exists(path):
print("WARNING: Path '%s' already exists; skipping" % path)
else:
otherwise(path) | python | def check_path(path, otherwise):
"""
Checks if a path exists. If it does, print a warning message; if not,
execute the `otherwise` callback argument.
"""
if os.path.exists(path):
print("WARNING: Path '%s' already exists; skipping" % path)
else:
otherwise(path) | [
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dailymuse/oz | oz/core/actions.py | config_maker | def config_maker(project_name, path):
"""Creates a config file based on the project name"""
with open(skeleton_path("config.py"), "r") as config_source:
config_content = config_source.read()
config_content = config_content.replace("__PROJECT_NAME__", project_name)
with open(path, "w") as config_dest:
config_dest.write(config_content) | python | def config_maker(project_name, path):
"""Creates a config file based on the project name"""
with open(skeleton_path("config.py"), "r") as config_source:
config_content = config_source.read()
config_content = config_content.replace("__PROJECT_NAME__", project_name)
with open(path, "w") as config_dest:
config_dest.write(config_content) | [
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dailymuse/oz | oz/core/actions.py | skeleton_path | def skeleton_path(parts):
"""Gets the path to a skeleton asset"""
return os.path.join(os.path.dirname(oz.__file__), "skeleton", parts) | python | def skeleton_path(parts):
"""Gets the path to a skeleton asset"""
return os.path.join(os.path.dirname(oz.__file__), "skeleton", parts) | [
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dailymuse/oz | oz/core/actions.py | init | def init(project_name):
"""Creates a new project"""
if not VALID_PROJECT_NAME.match(project_name):
print("Invalid project name. It may only contain letters, numbers and underscores.", file=sys.stderr)
return
check_path(project_name, functools.partial(shutil.copytree, skeleton_path("plugin")))
check_path("static", os.mkdir)
check_path("templates", os.mkdir)
check_path("config.py", functools.partial(config_maker, project_name)) | python | def init(project_name):
"""Creates a new project"""
if not VALID_PROJECT_NAME.match(project_name):
print("Invalid project name. It may only contain letters, numbers and underscores.", file=sys.stderr)
return
check_path(project_name, functools.partial(shutil.copytree, skeleton_path("plugin")))
check_path("static", os.mkdir)
check_path("templates", os.mkdir)
check_path("config.py", functools.partial(config_maker, project_name)) | [
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dailymuse/oz | oz/core/actions.py | server | def server():
"""Runs the server"""
tornado.log.enable_pretty_logging()
# Get and validate the server_type
server_type = oz.settings["server_type"]
if server_type not in [None, "wsgi", "asyncio", "twisted"]:
raise Exception("Unknown server type: %s" % server_type)
# Install the correct ioloop if necessary
if server_type == "asyncio":
from tornado.platform.asyncio import AsyncIOMainLoop
AsyncIOMainLoop().install()
elif server_type == "twisted":
from tornado.platform.twisted import TwistedIOLoop
TwistedIOLoop().install()
if server_type == "wsgi":
wsgi_app = tornado.wsgi.WSGIApplication(oz._routes, **oz.settings)
wsgi_srv = wsgiref.simple_server.make_server("", oz.settings["port"], wsgi_app)
wsgi_srv.serve_forever()
else:
web_app = tornado.web.Application(oz._routes, **oz.settings)
if oz.settings["ssl_cert_file"] != None and oz.settings["ssl_key_file"] != None:
ssl_options = {
"certfile": oz.settings["ssl_cert_file"],
"keyfile": oz.settings["ssl_key_file"],
"cert_reqs": oz.settings["ssl_cert_reqs"],
"ca_certs": oz.settings["ssl_ca_certs"]
}
else:
ssl_options = None
http_srv = tornado.httpserver.HTTPServer(
web_app,
ssl_options=ssl_options,
body_timeout=oz.settings["body_timeout"],
xheaders=oz.settings["xheaders"]
)
http_srv.bind(oz.settings["port"])
server_workers = oz.settings["server_workers"]
if server_workers > 1:
if oz.settings["debug"]:
print("WARNING: Debug is enabled, but multiple server workers have been configured. Only one server worker can run in debug mode.")
server_workers = 1
elif (server_type == "asyncio" or server_type == "twisted"):
print("WARNING: A non-default server type is being used, but multiple server workers have been configured. Only one server worker can run on a non-default server type.")
server_workers = 1
# Forks multiple sub-processes if server_workers > 1
http_srv.start(server_workers)
# Registers signal handles for graceful server shutdown
if oz.settings.get("use_graceful_shutdown"):
if server_type == "asyncio" or server_type == "twisted":
print("WARNING: Cannot enable graceful shutdown for asyncio or twisted server types.")
else:
# NOTE: Do not expect any logging to with certain tools (e.g., invoker),
# because they may quiet logs on SIGINT/SIGTERM
signal.signal(signal.SIGTERM, functools.partial(_shutdown_tornado_ioloop, http_srv))
signal.signal(signal.SIGINT, functools.partial(_shutdown_tornado_ioloop, http_srv))
# Starts the ioloops
if server_type == "asyncio":
import asyncio
asyncio.get_event_loop().run_forever()
elif server_type == "twisted":
from twisted.internet import reactor
reactor.run()
else:
from tornado import ioloop
ioloop.IOLoop.instance().start() | python | def server():
"""Runs the server"""
tornado.log.enable_pretty_logging()
# Get and validate the server_type
server_type = oz.settings["server_type"]
if server_type not in [None, "wsgi", "asyncio", "twisted"]:
raise Exception("Unknown server type: %s" % server_type)
# Install the correct ioloop if necessary
if server_type == "asyncio":
from tornado.platform.asyncio import AsyncIOMainLoop
AsyncIOMainLoop().install()
elif server_type == "twisted":
from tornado.platform.twisted import TwistedIOLoop
TwistedIOLoop().install()
if server_type == "wsgi":
wsgi_app = tornado.wsgi.WSGIApplication(oz._routes, **oz.settings)
wsgi_srv = wsgiref.simple_server.make_server("", oz.settings["port"], wsgi_app)
wsgi_srv.serve_forever()
else:
web_app = tornado.web.Application(oz._routes, **oz.settings)
if oz.settings["ssl_cert_file"] != None and oz.settings["ssl_key_file"] != None:
ssl_options = {
"certfile": oz.settings["ssl_cert_file"],
"keyfile": oz.settings["ssl_key_file"],
"cert_reqs": oz.settings["ssl_cert_reqs"],
"ca_certs": oz.settings["ssl_ca_certs"]
}
else:
ssl_options = None
http_srv = tornado.httpserver.HTTPServer(
web_app,
ssl_options=ssl_options,
body_timeout=oz.settings["body_timeout"],
xheaders=oz.settings["xheaders"]
)
http_srv.bind(oz.settings["port"])
server_workers = oz.settings["server_workers"]
if server_workers > 1:
if oz.settings["debug"]:
print("WARNING: Debug is enabled, but multiple server workers have been configured. Only one server worker can run in debug mode.")
server_workers = 1
elif (server_type == "asyncio" or server_type == "twisted"):
print("WARNING: A non-default server type is being used, but multiple server workers have been configured. Only one server worker can run on a non-default server type.")
server_workers = 1
# Forks multiple sub-processes if server_workers > 1
http_srv.start(server_workers)
# Registers signal handles for graceful server shutdown
if oz.settings.get("use_graceful_shutdown"):
if server_type == "asyncio" or server_type == "twisted":
print("WARNING: Cannot enable graceful shutdown for asyncio or twisted server types.")
else:
# NOTE: Do not expect any logging to with certain tools (e.g., invoker),
# because they may quiet logs on SIGINT/SIGTERM
signal.signal(signal.SIGTERM, functools.partial(_shutdown_tornado_ioloop, http_srv))
signal.signal(signal.SIGINT, functools.partial(_shutdown_tornado_ioloop, http_srv))
# Starts the ioloops
if server_type == "asyncio":
import asyncio
asyncio.get_event_loop().run_forever()
elif server_type == "twisted":
from twisted.internet import reactor
reactor.run()
else:
from tornado import ioloop
ioloop.IOLoop.instance().start() | [
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dailymuse/oz | oz/core/actions.py | repl | def repl():
"""Runs an IPython repl with some context"""
try:
import IPython
except:
print("ERROR: IPython is not installed. Please install it to use the repl.", file=sys.stderr)
raise
IPython.embed(user_ns=dict(
settings=oz.settings,
actions=oz._actions,
uimodules=oz._uimodules,
routes=oz._routes,
)) | python | def repl():
"""Runs an IPython repl with some context"""
try:
import IPython
except:
print("ERROR: IPython is not installed. Please install it to use the repl.", file=sys.stderr)
raise
IPython.embed(user_ns=dict(
settings=oz.settings,
actions=oz._actions,
uimodules=oz._uimodules,
routes=oz._routes,
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michaelpb/omnic | omnic/conversion/resolvergraph.py | ResolverGraph.find_resource_url_basename | def find_resource_url_basename(self, resource_url):
'''
Figure out path basename for given resource_url
'''
scheme = resource_url.parsed.scheme
if scheme in ('http', 'https', 'file'):
return _get_basename_based_on_url(resource_url)
elif scheme in ('git', 'git+https', 'git+http'):
if len(resource_url.args) == 2:
# For now, git has 2 positional args, hash and path
git_tree, subpath = resource_url.args
basename = os.path.basename(subpath)
if basename:
return basename # subpath was not '/' or ''
return _get_basename_based_on_url(resource_url) | python | def find_resource_url_basename(self, resource_url):
'''
Figure out path basename for given resource_url
'''
scheme = resource_url.parsed.scheme
if scheme in ('http', 'https', 'file'):
return _get_basename_based_on_url(resource_url)
elif scheme in ('git', 'git+https', 'git+http'):
if len(resource_url.args) == 2:
# For now, git has 2 positional args, hash and path
git_tree, subpath = resource_url.args
basename = os.path.basename(subpath)
if basename:
return basename # subpath was not '/' or ''
return _get_basename_based_on_url(resource_url) | [
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michaelpb/omnic | omnic/conversion/resolvergraph.py | ResolverGraph.find_destination_type | def find_destination_type(self, resource_url):
'''
Given a resource_url, figure out what it would resolve into
'''
resolvers = self.converters.values()
for resolver in resolvers:
# Not all resolvers are opinionated about destination types
if not hasattr(resolver, 'get_destination_type'):
continue
destination_type = resolver.get_destination_type(resource_url)
if destination_type:
return destination_type | python | def find_destination_type(self, resource_url):
'''
Given a resource_url, figure out what it would resolve into
'''
resolvers = self.converters.values()
for resolver in resolvers:
# Not all resolvers are opinionated about destination types
if not hasattr(resolver, 'get_destination_type'):
continue
destination_type = resolver.get_destination_type(resource_url)
if destination_type:
return destination_type | [
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michaelpb/omnic | omnic/conversion/resolvergraph.py | ResolverGraph.download | async def download(self, resource_url):
'''
Download given Resource URL by finding path through graph and applying
each step
'''
resolver_path = self.find_path_from_url(resource_url)
await self.apply_resolver_path(resource_url, resolver_path) | python | async def download(self, resource_url):
'''
Download given Resource URL by finding path through graph and applying
each step
'''
resolver_path = self.find_path_from_url(resource_url)
await self.apply_resolver_path(resource_url, resolver_path) | [
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biocore/burrito-fillings | bfillings/parsinsert.py | insert_sequences_into_tree | def insert_sequences_into_tree(aln, moltype, params={}):
"""Returns a tree from placement of sequences
"""
# convert aln to phy since seq_names need fixed to run through parsinsert
new_aln=get_align_for_phylip(StringIO(aln))
# convert aln to fasta in case it is not already a fasta file
aln2 = Alignment(new_aln)
seqs = aln2.toFasta()
parsinsert_app = ParsInsert(params=params)
result = parsinsert_app(seqs)
# parse tree
tree = DndParser(result['Tree'].read(), constructor=PhyloNode)
# cleanup files
result.cleanUp()
return tree | python | def insert_sequences_into_tree(aln, moltype, params={}):
"""Returns a tree from placement of sequences
"""
# convert aln to phy since seq_names need fixed to run through parsinsert
new_aln=get_align_for_phylip(StringIO(aln))
# convert aln to fasta in case it is not already a fasta file
aln2 = Alignment(new_aln)
seqs = aln2.toFasta()
parsinsert_app = ParsInsert(params=params)
result = parsinsert_app(seqs)
# parse tree
tree = DndParser(result['Tree'].read(), constructor=PhyloNode)
# cleanup files
result.cleanUp()
return tree | [
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biocore/burrito-fillings | bfillings/parsinsert.py | ParsInsert._get_result_paths | def _get_result_paths(self,data):
""" Get the resulting tree"""
result = {}
result['Tree'] = ResultPath(Path=splitext(self._input_filename)[0] + \
'.tree')
return result | python | def _get_result_paths(self,data):
""" Get the resulting tree"""
result = {}
result['Tree'] = ResultPath(Path=splitext(self._input_filename)[0] + \
'.tree')
return result | [
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michaelpb/omnic | omnic/conversion/resolver.py | download | async def download(resource_url):
'''
Download given resource_url
'''
scheme = resource_url.parsed.scheme
if scheme in ('http', 'https'):
await download_http(resource_url)
elif scheme in ('git', 'git+https', 'git+http'):
await download_git(resource_url)
else:
raise ValueError('Unknown URL scheme: "%s"' % scheme) | python | async def download(resource_url):
'''
Download given resource_url
'''
scheme = resource_url.parsed.scheme
if scheme in ('http', 'https'):
await download_http(resource_url)
elif scheme in ('git', 'git+https', 'git+http'):
await download_git(resource_url)
else:
raise ValueError('Unknown URL scheme: "%s"' % scheme) | [
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imu-hupeng/cos-python3-sdk | cos_lib3/cos.py | CosBucket.create_folder | def create_folder(self, dir_name):
"""创建目录(https://www.qcloud.com/document/product/436/6061)
:param dir_name:要创建的目录的目录的名称
:return 返回True创建成功，返回False创建失败
"""
if dir_name[0] == '/':
dir_name = dir_name[1:len(dir_name)]
self.url = "http://<Region>.file.myqcloud.com" + "/files/v2/<appid>/<bucket_name>/<dir_name>/"
self.url = self.url.replace("<Region>", self.config.region).replace("<appid>", str(self.config.app_id))
self.url = str(self.url).replace("<bucket_name>", self.config.bucket).replace("<dir_name>", dir_name)
self.headers['Authorization'] = CosAuth(self.config).sign_more(self.config.bucket, '', 30 )
response, content = self.http.request(uri=self.url, method='POST', body='{"op": "create", "biz_attr": ""}', headers=self.headers)
if eval(content.decode('utf8')).get("code") == 0:
return True
else:
return False | python | def create_folder(self, dir_name):
"""创建目录(https://www.qcloud.com/document/product/436/6061)
:param dir_name:要创建的目录的目录的名称
:return 返回True创建成功，返回False创建失败
"""
if dir_name[0] == '/':
dir_name = dir_name[1:len(dir_name)]
self.url = "http://<Region>.file.myqcloud.com" + "/files/v2/<appid>/<bucket_name>/<dir_name>/"
self.url = self.url.replace("<Region>", self.config.region).replace("<appid>", str(self.config.app_id))
self.url = str(self.url).replace("<bucket_name>", self.config.bucket).replace("<dir_name>", dir_name)
self.headers['Authorization'] = CosAuth(self.config).sign_more(self.config.bucket, '', 30 )
response, content = self.http.request(uri=self.url, method='POST', body='{"op": "create", "biz_attr": ""}', headers=self.headers)
if eval(content.decode('utf8')).get("code") == 0:
return True
else:
return False | [
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imu-hupeng/cos-python3-sdk | cos_lib3/cos.py | CosBucket.list_folder | def list_folder(self, dir_name=None, prefix=None, num=1000, context=None):
"""列目录(https://www.qcloud.com/document/product/436/6062)
:param dir_name:文件夹名称
:param prefix:前缀
:param num:查询的文件的数量，最大支持1000，默认查询数量为1000
:param context:翻页标志，将上次查询结果的context的字段传入，即可实现翻页的功能
:return 查询结果，为json格式
"""
if dir_name[0] == '/':
dir_name = dir_name[1:len(dir_name)]
self.url = 'http://<Region>.file.myqcloud.com/files/v2/<appid>/<bucket_name>/'
self.url = self.url.replace("<Region>", self.config.region).replace("<appid>", str(self.config.app_id)).replace("<bucket_name>", self.config.bucket)
if dir_name is not None:
self.url = self.url + str(dir_name) + "/"
if prefix is not None:
self.url = self.url + str(prefix)
self.url = self.url + "?op=list&num=" + str(num)
if context is not None:
self.url = self.url + '&context=' + str(context)
self.headers['Authorization'] = CosAuth(self.config).sign_more(self.config.bucket, '', 30)
response, content = self.http.request(uri=self.url, method='GET', headers=self.headers)
return content.decode("utf8") | python | def list_folder(self, dir_name=None, prefix=None, num=1000, context=None):
"""列目录(https://www.qcloud.com/document/product/436/6062)
:param dir_name:文件夹名称
:param prefix:前缀
:param num:查询的文件的数量，最大支持1000，默认查询数量为1000
:param context:翻页标志，将上次查询结果的context的字段传入，即可实现翻页的功能
:return 查询结果，为json格式
"""
if dir_name[0] == '/':
dir_name = dir_name[1:len(dir_name)]
self.url = 'http://<Region>.file.myqcloud.com/files/v2/<appid>/<bucket_name>/'
self.url = self.url.replace("<Region>", self.config.region).replace("<appid>", str(self.config.app_id)).replace("<bucket_name>", self.config.bucket)
if dir_name is not None:
self.url = self.url + str(dir_name) + "/"
if prefix is not None:
self.url = self.url + str(prefix)
self.url = self.url + "?op=list&num=" + str(num)
if context is not None:
self.url = self.url + '&context=' + str(context)
self.headers['Authorization'] = CosAuth(self.config).sign_more(self.config.bucket, '', 30)
response, content = self.http.request(uri=self.url, method='GET', headers=self.headers)
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imu-hupeng/cos-python3-sdk | cos_lib3/cos.py | CosBucket.query_folder | def query_folder(self, dir_name):
"""查询目录属性(https://www.qcloud.com/document/product/436/6063)
:param dir_name:查询的目录的名称
:return:查询出来的结果，为json格式
"""
if dir_name[0] == '/':
dir_name = dir_name[1:len(dir_name)]
self.url = 'http://' + self.config.region + '.file.myqcloud.com' + '/files/v2/' + str(self.config.app_id) + '/' + self.config.bucket + '/' + dir_name + '/?op=stat'
self.headers['Authorization'] = CosAuth(self.config).sign_more(self.config.bucket, '', 30)
reponse, content = self.http.request(uri=self.url, method='GET',headers=self.headers)
return content.decode("utf8") | python | def query_folder(self, dir_name):
"""查询目录属性(https://www.qcloud.com/document/product/436/6063)
:param dir_name:查询的目录的名称
:return:查询出来的结果，为json格式
"""
if dir_name[0] == '/':
dir_name = dir_name[1:len(dir_name)]
self.url = 'http://' + self.config.region + '.file.myqcloud.com' + '/files/v2/' + str(self.config.app_id) + '/' + self.config.bucket + '/' + dir_name + '/?op=stat'
self.headers['Authorization'] = CosAuth(self.config).sign_more(self.config.bucket, '', 30)
reponse, content = self.http.request(uri=self.url, method='GET',headers=self.headers)
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imu-hupeng/cos-python3-sdk | cos_lib3/cos.py | CosBucket.upload_file | def upload_file(self, real_file_path, file_name, dir_name=None):
"""简单上传文件(https://www.qcloud.com/document/product/436/6066)
:param real_file_path: 文件的物理地址
:param file_name: 文件名称
:param dir_name: 文件夹名称（可选）
:return:json数据串
"""
if dir_name is not None and dir_name[0] == '/':
dir_name = dir_name[1:len(dir_name)]
if dir_name is None:
dir_name = ""
self.url = 'http://' + self.config.region + '.file.myqcloud.com/files/v2/' + str(self.config.app_id) + '/' + self.config.bucket
if dir_name is not None:
self.url = self.url + '/' + dir_name
self.url = self.url + '/' + file_name
headers = {}
headers['Authorization'] = CosAuth(self.config).sign_more(self.config.bucket, '', 30)
files = {'file': ('', open(real_file_path, 'rb'))}
r = requests.post(url=self.url, data={'op': 'upload', 'biz_attr': '', 'insertOnly': '0'}, files={
'filecontent': (real_file_path, open(real_file_path, 'rb'), 'application/octet-stream')}, headers=headers)
return str(eval(r.content.decode('utf8')).get('data')) | python | def upload_file(self, real_file_path, file_name, dir_name=None):
"""简单上传文件(https://www.qcloud.com/document/product/436/6066)
:param real_file_path: 文件的物理地址
:param file_name: 文件名称
:param dir_name: 文件夹名称（可选）
:return:json数据串
"""
if dir_name is not None and dir_name[0] == '/':
dir_name = dir_name[1:len(dir_name)]
if dir_name is None:
dir_name = ""
self.url = 'http://' + self.config.region + '.file.myqcloud.com/files/v2/' + str(self.config.app_id) + '/' + self.config.bucket
if dir_name is not None:
self.url = self.url + '/' + dir_name
self.url = self.url + '/' + file_name
headers = {}
headers['Authorization'] = CosAuth(self.config).sign_more(self.config.bucket, '', 30)
files = {'file': ('', open(real_file_path, 'rb'))}
r = requests.post(url=self.url, data={'op': 'upload', 'biz_attr': '', 'insertOnly': '0'}, files={
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return str(eval(r.content.decode('utf8')).get('data')) | [
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imu-hupeng/cos-python3-sdk | cos_lib3/cos.py | CosBucket.upload_slice_file | def upload_slice_file(self, real_file_path, slice_size, file_name, offset=0, dir_name=None):
"""
此分片上传代码由GitHub用户a270443177(https://github.com/a270443177)友情提供
:param real_file_path:
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:param dir_name:
:return:
"""
if dir_name is not None and dir_name[0] == '/':
dir_name = dir_name[1:len(dir_name)]
if dir_name is None:
dir_name = ""
self.url = 'http://' + self.config.region + '.file.myqcloud.com/files/v2/' + str(
self.config.app_id) + '/' + self.config.bucket
if dir_name is not None:
self.url = self.url + '/' + dir_name
self.url = self.url + '/' + file_name
file_size = os.path.getsize(real_file_path)
session = self._upload_slice_control(file_size=file_size, slice_size=slice_size)
with open(real_file_path, 'rb') as local_file:
while offset < file_size:
file_content = local_file.read(slice_size)
self._upload_slice_data(filecontent=file_content, session=session, offset=offset)
offset += slice_size
r = self._upload_slice_finish(session=session, file_size=file_size)
return r | python | def upload_slice_file(self, real_file_path, slice_size, file_name, offset=0, dir_name=None):
"""
此分片上传代码由GitHub用户a270443177(https://github.com/a270443177)友情提供
:param real_file_path:
:param slice_size:
:param file_name:
:param offset:
:param dir_name:
:return:
"""
if dir_name is not None and dir_name[0] == '/':
dir_name = dir_name[1:len(dir_name)]
if dir_name is None:
dir_name = ""
self.url = 'http://' + self.config.region + '.file.myqcloud.com/files/v2/' + str(
self.config.app_id) + '/' + self.config.bucket
if dir_name is not None:
self.url = self.url + '/' + dir_name
self.url = self.url + '/' + file_name
file_size = os.path.getsize(real_file_path)
session = self._upload_slice_control(file_size=file_size, slice_size=slice_size)
with open(real_file_path, 'rb') as local_file:
while offset < file_size:
file_content = local_file.read(slice_size)
self._upload_slice_data(filecontent=file_content, session=session, offset=offset)
offset += slice_size
r = self._upload_slice_finish(session=session, file_size=file_size)
return r | [
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imu-hupeng/cos-python3-sdk | cos_lib3/cos.py | CosBucket.upload_file_from_url | def upload_file_from_url(self, url, file_name, dir_name=None):
"""简单上传文件(https://www.qcloud.com/document/product/436/6066)
:param url: 文件url地址
:param file_name: 文件名称
:param dir_name: 文件夹名称（可选）
:return:json数据串
"""
real_file_name = str(int(time.time()*1000))
urllib.request.urlretrieve(url, real_file_name)
data = self.upload_file(real_file_name, file_name, dir_name)
os.remove(real_file_name)
return data | python | def upload_file_from_url(self, url, file_name, dir_name=None):
"""简单上传文件(https://www.qcloud.com/document/product/436/6066)
:param url: 文件url地址
:param file_name: 文件名称
:param dir_name: 文件夹名称（可选）
:return:json数据串
"""
real_file_name = str(int(time.time()*1000))
urllib.request.urlretrieve(url, real_file_name)
data = self.upload_file(real_file_name, file_name, dir_name)
os.remove(real_file_name)
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imu-hupeng/cos-python3-sdk | cos_lib3/cos.py | CosAuth.sign_more | def sign_more(self, bucket, cos_path, expired):
"""多次签名(针对上传文件，创建目录, 获取文件目录属性, 拉取目录列表)
:param bucket: bucket名称
:param cos_path: 要操作的cos路径, 以'/'开始
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:return: 签名字符串
"""
return self.app_sign(bucket, cos_path, expired) | python | def sign_more(self, bucket, cos_path, expired):
"""多次签名(针对上传文件，创建目录, 获取文件目录属性, 拉取目录列表)
:param bucket: bucket名称
:param cos_path: 要操作的cos路径, 以'/'开始
:param expired: 签名过期时间, UNIX时间戳, 如想让签名在30秒后过期, 即可将expired设成当前时间加上30秒
:return: 签名字符串
"""
return self.app_sign(bucket, cos_path, expired) | [
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imu-hupeng/cos-python3-sdk | cos_lib3/cos.py | CosAuth.sign_download | def sign_download(self, bucket, cos_path, expired):
"""下载签名(用于获取后拼接成下载链接，下载私有bucket的文件)
:param bucket: bucket名称
:param cos_path: 要下载的cos文件路径, 以'/'开始
:param expired: 签名过期时间, UNIX时间戳, 如想让签名在30秒后过期, 即可将expired设成当前时间加上30秒
:return: 签名字符串
"""
return self.app_sign(bucket, cos_path, expired, False) | python | def sign_download(self, bucket, cos_path, expired):
"""下载签名(用于获取后拼接成下载链接，下载私有bucket的文件)
:param bucket: bucket名称
:param cos_path: 要下载的cos文件路径, 以'/'开始
:param expired: 签名过期时间, UNIX时间戳, 如想让签名在30秒后过期, 即可将expired设成当前时间加上30秒
:return: 签名字符串
"""
return self.app_sign(bucket, cos_path, expired, False) | [
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scott-maddox/openbandparams | src/openbandparams/iii_v_zinc_blende_alloy.py | IIIVZincBlendeAlloy.strained_001 | def strained_001(self, target):
'''
Returns an instance of ``IIIVZincBlendeStrained001``, which is a
biaxial-strained III-V zinc blende binary alloy grown on a (001)
surface.
Parameters
----------
target : Alloy with ``a`` parameter or float
Growth substrate, assumed to have a (001) surface, or out-of-plane
strain, which is negative for tensile strain and positive for
compressive strain. This is the strain measured by X-ray
diffraction (XRD) symmetric omega-2theta scans.
'''
if isinstance(target, Alloy):
return IIIVZincBlendeStrained001(unstrained=self,
substrate=target)
else:
return IIIVZincBlendeStrained001(unstrained=self,
strain_out_of_plane=target) | python | def strained_001(self, target):
'''
Returns an instance of ``IIIVZincBlendeStrained001``, which is a
biaxial-strained III-V zinc blende binary alloy grown on a (001)
surface.
Parameters
----------
target : Alloy with ``a`` parameter or float
Growth substrate, assumed to have a (001) surface, or out-of-plane
strain, which is negative for tensile strain and positive for
compressive strain. This is the strain measured by X-ray
diffraction (XRD) symmetric omega-2theta scans.
'''
if isinstance(target, Alloy):
return IIIVZincBlendeStrained001(unstrained=self,
substrate=target)
else:
return IIIVZincBlendeStrained001(unstrained=self,
strain_out_of_plane=target) | [
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scott-maddox/openbandparams | src/openbandparams/iii_v_zinc_blende_alloy.py | IIIVZincBlendeAlloy.Eg | def Eg(self, **kwargs):
'''
Returns the bandgap, Eg, in eV at a given
temperature, T, in K (default=300.).
'''
return min(self.Eg_Gamma(**kwargs),
self.Eg_L(**kwargs),
self.Eg_X(**kwargs)) | python | def Eg(self, **kwargs):
'''
Returns the bandgap, Eg, in eV at a given
temperature, T, in K (default=300.).
'''
return min(self.Eg_Gamma(**kwargs),
self.Eg_L(**kwargs),
self.Eg_X(**kwargs)) | [
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scott-maddox/openbandparams | src/openbandparams/iii_v_zinc_blende_alloy.py | IIIVZincBlendeAlloy.F | def F(self, **kwargs):
'''
Returns the Kane remote-band parameter, `F`, calculated from
`Eg_Gamma_0`, `Delta_SO`, `Ep`, and `meff_e_Gamma_0`.
'''
Eg = self.Eg_Gamma_0(**kwargs)
Delta_SO = self.Delta_SO(**kwargs)
Ep = self.Ep(**kwargs)
meff = self.meff_e_Gamma_0(**kwargs)
return (1./meff-1-(Ep*(Eg+2.*Delta_SO/3.))/(Eg*(Eg+Delta_SO)))/2 | python | def F(self, **kwargs):
'''
Returns the Kane remote-band parameter, `F`, calculated from
`Eg_Gamma_0`, `Delta_SO`, `Ep`, and `meff_e_Gamma_0`.
'''
Eg = self.Eg_Gamma_0(**kwargs)
Delta_SO = self.Delta_SO(**kwargs)
Ep = self.Ep(**kwargs)
meff = self.meff_e_Gamma_0(**kwargs)
return (1./meff-1-(Ep*(Eg+2.*Delta_SO/3.))/(Eg*(Eg+Delta_SO)))/2 | [
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scott-maddox/openbandparams | src/openbandparams/iii_v_zinc_blende_alloy.py | IIIVZincBlendeAlloy.a | def a(self, **kwargs):
'''
Returns the lattice parameter, a, in Angstroms at a given
temperature, `T`, in Kelvin (default: 300 K).
'''
T = kwargs.get('T', 300.)
return (self.a_300K(**kwargs) +
self.thermal_expansion(**kwargs) * (T - 300.)) | python | def a(self, **kwargs):
'''
Returns the lattice parameter, a, in Angstroms at a given
temperature, `T`, in Kelvin (default: 300 K).
'''
T = kwargs.get('T', 300.)
return (self.a_300K(**kwargs) +
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scott-maddox/openbandparams | src/openbandparams/iii_v_zinc_blende_alloy.py | IIIVZincBlendeAlloy.meff_SO | def meff_SO(self, **kwargs):
'''
Returns the split-off hole effective mass
calculated from Eg_Gamma(T), Delta_SO, Ep and F.
Interpolation of Eg_Gamma(T), Delta_SO, Ep and luttinger1, and
then calculation of meff_SO is recommended for alloys.
'''
Eg = self.Eg_Gamma(**kwargs)
Delta_SO = self.Delta_SO(**kwargs)
Ep = self.Ep(**kwargs)
luttinger1 = self.luttinger1(**kwargs)
return 1./(luttinger1 - (Ep*Delta_SO)/(3*Eg*(Eg+Delta_SO))) | python | def meff_SO(self, **kwargs):
'''
Returns the split-off hole effective mass
calculated from Eg_Gamma(T), Delta_SO, Ep and F.
Interpolation of Eg_Gamma(T), Delta_SO, Ep and luttinger1, and
then calculation of meff_SO is recommended for alloys.
'''
Eg = self.Eg_Gamma(**kwargs)
Delta_SO = self.Delta_SO(**kwargs)
Ep = self.Ep(**kwargs)
luttinger1 = self.luttinger1(**kwargs)
return 1./(luttinger1 - (Ep*Delta_SO)/(3*Eg*(Eg+Delta_SO))) | [
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scott-maddox/openbandparams | src/openbandparams/iii_v_zinc_blende_alloy.py | IIIVZincBlendeAlloy.meff_e_Gamma | def meff_e_Gamma(self, **kwargs):
'''
Returns the electron effective mass in the Gamma-valley
calculated from Eg_Gamma(T), Delta_SO, Ep and F.
Interpolation of Eg_Gamma(T), Delta_SO, Ep and F, and
then calculation of meff_e_Gamma is recommended for alloys.
'''
Eg = self.Eg_Gamma(**kwargs)
Delta_SO = self.Delta_SO(**kwargs)
Ep = self.Ep(**kwargs)
F = self.F(**kwargs)
return 1./((1.+2.*F)+(Ep*(Eg+2.*Delta_SO/3.))/(Eg*(Eg+Delta_SO))) | python | def meff_e_Gamma(self, **kwargs):
'''
Returns the electron effective mass in the Gamma-valley
calculated from Eg_Gamma(T), Delta_SO, Ep and F.
Interpolation of Eg_Gamma(T), Delta_SO, Ep and F, and
then calculation of meff_e_Gamma is recommended for alloys.
'''
Eg = self.Eg_Gamma(**kwargs)
Delta_SO = self.Delta_SO(**kwargs)
Ep = self.Ep(**kwargs)
F = self.F(**kwargs)
return 1./((1.+2.*F)+(Ep*(Eg+2.*Delta_SO/3.))/(Eg*(Eg+Delta_SO))) | [
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scott-maddox/openbandparams | src/openbandparams/iii_v_zinc_blende_alloy.py | IIIVZincBlendeAlloy.meff_hh_110 | def meff_hh_110(self, **kwargs):
'''
Returns the heavy-hole band effective mass in the [110] direction,
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'''
return 2. / (2 * self.luttinger1(**kwargs) - self.luttinger2(**kwargs)
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'''
Returns the heavy-hole band effective mass in the [110] direction,
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'''
return 2. / (2 * self.luttinger1(**kwargs) - self.luttinger2(**kwargs)
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scott-maddox/openbandparams | src/openbandparams/iii_v_zinc_blende_alloy.py | IIIVZincBlendeAlloy.meff_lh_110 | def meff_lh_110(self, **kwargs):
'''
Returns the light-hole band effective mass in the [110] direction,
meff_lh_110, in units of electron mass.
'''
return 2. / (2 * self.luttinger1(**kwargs) + self.luttinger2(**kwargs)
+ 3 * self.luttinger3(**kwargs)) | python | def meff_lh_110(self, **kwargs):
'''
Returns the light-hole band effective mass in the [110] direction,
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'''
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scott-maddox/openbandparams | src/openbandparams/iii_v_zinc_blende_alloy.py | IIIVZincBlendeAlloy.nonparabolicity | def nonparabolicity(self, **kwargs):
'''
Returns the Kane band nonparabolicity parameter for the Gamma-valley.
'''
Eg = self.Eg_Gamma(**kwargs)
meff = self.meff_e_Gamma(**kwargs)
T = kwargs.get('T', 300.)
return k*T/Eg * (1 - meff)**2 | python | def nonparabolicity(self, **kwargs):
'''
Returns the Kane band nonparabolicity parameter for the Gamma-valley.
'''
Eg = self.Eg_Gamma(**kwargs)
meff = self.meff_e_Gamma(**kwargs)
T = kwargs.get('T', 300.)
return k*T/Eg * (1 - meff)**2 | [
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castelao/oceansdb | oceansdb/etopo.py | ETOPO_var_nc.crop | def crop(self, lat, lon, var):
""" Crop a subset of the dataset for each var
Given doy, depth, lat and lon, it returns the smallest subset
that still contains the requested coordinates inside it.
It handels special cases like a region around greenwich and
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Accepts 0 to 360 and -180 to 180 longitude reference.
It extends time and longitude coordinates, so simplify the use
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a longitude sequence like [352, 358, 364, 369, 380].
"""
dims, idx = cropIndices(self.dims, lat, lon)
subset = {}
for v in var:
subset = {v: self.ncs[0][v][idx['yn'], idx['xn']]}
return subset, dims | python | def crop(self, lat, lon, var):
""" Crop a subset of the dataset for each var
Given doy, depth, lat and lon, it returns the smallest subset
that still contains the requested coordinates inside it.
It handels special cases like a region around greenwich and
the international date line.
Accepts 0 to 360 and -180 to 180 longitude reference.
It extends time and longitude coordinates, so simplify the use
of series. For example, a ship track can be requested with
a longitude sequence like [352, 358, 364, 369, 380].
"""
dims, idx = cropIndices(self.dims, lat, lon)
subset = {}
for v in var:
subset = {v: self.ncs[0][v][idx['yn'], idx['xn']]}
return subset, dims | [
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castelao/oceansdb | oceansdb/etopo.py | ETOPO_var_nc.interpolate | def interpolate(self, lat, lon, var):
""" Interpolate each var on the coordinates requested
"""
subset, dims = self.crop(lat, lon, var)
if np.all([y in dims['lat'] for y in lat]) & \
np.all([x in dims['lon'] for x in lon]):
yn = np.nonzero([y in lat for y in dims['lat']])[0]
xn = np.nonzero([x in lon for x in dims['lon']])[0]
output = {}
for v in subset:
# output[v] = subset[v][dn, zn, yn, xn]
# Seriously that this is the way to do it?!!??
output[v] = subset[v][:, xn][yn]
return output
# The output coordinates shall be created only once.
points_out = []
for latn in lat:
for lonn in lon:
points_out.append([latn, lonn])
points_out = np.array(points_out)
output = {}
for v in var:
output[v] = ma.masked_all(
(lat.size, lon.size),
dtype=subset[v].dtype)
# The valid data
idx = np.nonzero(~ma.getmaskarray(subset[v]))
if idx[0].size > 0:
points = np.array([
dims['lat'][idx[0]], dims['lon'][idx[1]]]).T
values = subset[v][idx]
# Interpolate along the dimensions that have more than one
# position, otherwise it means that the output is exactly
# on that coordinate.
ind = np.array(
[np.unique(points[:, i]).size > 1 for i in
range(points.shape[1])])
assert ind.any()
values_out = griddata(
np.atleast_1d(np.squeeze(points[:, ind])),
values,
np.atleast_1d(np.squeeze(points_out[:, ind]))
)
# Remap the interpolated value back into a 4D array
idx = np.isfinite(values_out)
for [y, x], out in zip(points_out[idx], values_out[idx]):
output[v][y==lat, x==lon] = out
return output | python | def interpolate(self, lat, lon, var):
""" Interpolate each var on the coordinates requested
"""
subset, dims = self.crop(lat, lon, var)
if np.all([y in dims['lat'] for y in lat]) & \
np.all([x in dims['lon'] for x in lon]):
yn = np.nonzero([y in lat for y in dims['lat']])[0]
xn = np.nonzero([x in lon for x in dims['lon']])[0]
output = {}
for v in subset:
# output[v] = subset[v][dn, zn, yn, xn]
# Seriously that this is the way to do it?!!??
output[v] = subset[v][:, xn][yn]
return output
# The output coordinates shall be created only once.
points_out = []
for latn in lat:
for lonn in lon:
points_out.append([latn, lonn])
points_out = np.array(points_out)
output = {}
for v in var:
output[v] = ma.masked_all(
(lat.size, lon.size),
dtype=subset[v].dtype)
# The valid data
idx = np.nonzero(~ma.getmaskarray(subset[v]))
if idx[0].size > 0:
points = np.array([
dims['lat'][idx[0]], dims['lon'][idx[1]]]).T
values = subset[v][idx]
# Interpolate along the dimensions that have more than one
# position, otherwise it means that the output is exactly
# on that coordinate.
ind = np.array(
[np.unique(points[:, i]).size > 1 for i in
range(points.shape[1])])
assert ind.any()
values_out = griddata(
np.atleast_1d(np.squeeze(points[:, ind])),
values,
np.atleast_1d(np.squeeze(points_out[:, ind]))
)
# Remap the interpolated value back into a 4D array
idx = np.isfinite(values_out)
for [y, x], out in zip(points_out[idx], values_out[idx]):
output[v][y==lat, x==lon] = out
return output | [
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michaelpb/omnic | omnic/conversion/graph.py | ConverterGraph._setup_converter_graph | def _setup_converter_graph(self, converter_list, prune_converters):
'''
Set up directed conversion graph, pruning unavailable converters as
necessary
'''
for converter in converter_list:
if prune_converters:
try:
converter.configure()
except ConverterUnavailable as e:
log.warning('%s unavailable: %s' %
(converter.__class__.__name__, str(e)))
continue
for in_ in converter.inputs:
for out in converter.outputs:
self.dgraph.add_edge(in_, out, converter.cost)
self.converters[(in_, out)] = converter
if hasattr(converter, 'direct_outputs'):
self._setup_direct_converter(converter) | python | def _setup_converter_graph(self, converter_list, prune_converters):
'''
Set up directed conversion graph, pruning unavailable converters as
necessary
'''
for converter in converter_list:
if prune_converters:
try:
converter.configure()
except ConverterUnavailable as e:
log.warning('%s unavailable: %s' %
(converter.__class__.__name__, str(e)))
continue
for in_ in converter.inputs:
for out in converter.outputs:
self.dgraph.add_edge(in_, out, converter.cost)
self.converters[(in_, out)] = converter
if hasattr(converter, 'direct_outputs'):
self._setup_direct_converter(converter) | [
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michaelpb/omnic | omnic/conversion/graph.py | ConverterGraph._setup_preferred_paths | def _setup_preferred_paths(self, preferred_conversion_paths):
'''
Add given valid preferred conversion paths
'''
for path in preferred_conversion_paths:
for pair in pair_looper(path):
if pair not in self.converters:
log.warning('Invalid conversion path %s, unknown step %s' %
(repr(path), repr(pair)))
break
else:
# If it did not break, then add to dgraph
self.dgraph.add_preferred_path(*path) | python | def _setup_preferred_paths(self, preferred_conversion_paths):
'''
Add given valid preferred conversion paths
'''
for path in preferred_conversion_paths:
for pair in pair_looper(path):
if pair not in self.converters:
log.warning('Invalid conversion path %s, unknown step %s' %
(repr(path), repr(pair)))
break
else:
# If it did not break, then add to dgraph
self.dgraph.add_preferred_path(*path) | [
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michaelpb/omnic | omnic/conversion/graph.py | ConverterGraph._setup_profiles | def _setup_profiles(self, conversion_profiles):
'''
Add given conversion profiles checking for invalid profiles
'''
# Check for invalid profiles
for key, path in conversion_profiles.items():
if isinstance(path, str):
path = (path, )
for left, right in pair_looper(path):
pair = (_format(left), _format(right))
if pair not in self.converters:
msg = 'Invalid conversion profile %s, unknown step %s'
log.warning(msg % (repr(key), repr(pair)))
break
else:
# If it did not break, then add to conversion profiles
self.conversion_profiles[key] = path | python | def _setup_profiles(self, conversion_profiles):
'''
Add given conversion profiles checking for invalid profiles
'''
# Check for invalid profiles
for key, path in conversion_profiles.items():
if isinstance(path, str):
path = (path, )
for left, right in pair_looper(path):
pair = (_format(left), _format(right))
if pair not in self.converters:
msg = 'Invalid conversion profile %s, unknown step %s'
log.warning(msg % (repr(key), repr(pair)))
break
else:
# If it did not break, then add to conversion profiles
self.conversion_profiles[key] = path | [
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michaelpb/omnic | omnic/conversion/graph.py | ConverterGraph._setup_direct_converter | def _setup_direct_converter(self, converter):
'''
Given a converter, set up the direct_output routes for conversions,
which is used for transcoding between similar datatypes.
'''
inputs = (
converter.direct_inputs
if hasattr(converter, 'direct_inputs')
else converter.inputs
)
for in_ in inputs:
for out in converter.direct_outputs:
self.direct_converters[(in_, out)] = converter | python | def _setup_direct_converter(self, converter):
'''
Given a converter, set up the direct_output routes for conversions,
which is used for transcoding between similar datatypes.
'''
inputs = (
converter.direct_inputs
if hasattr(converter, 'direct_inputs')
else converter.inputs
)
for in_ in inputs:
for out in converter.direct_outputs:
self.direct_converters[(in_, out)] = converter | [
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michaelpb/omnic | omnic/conversion/graph.py | ConverterGraph.find_path | def find_path(self, in_, out):
'''
Given an input and output TypeString, produce a graph traversal,
keeping in mind special options like Conversion Profiles, Preferred
Paths, and Direct Conversions.
'''
if in_.arguments:
raise ValueError('Cannot originate path in argumented TypeString')
# Determine conversion profile. This is either simply the output, OR,
# if a custom profile has been specified for this output, that custom
# path or type is used.
profile = self.conversion_profiles.get(str(out), str(out))
if isinstance(profile, str):
profile = (profile, )
types_by_format = {_format(s): TypeString(s) for s in profile}
# Normalize input and output types to string
in_str = str(in_)
out_str = _format(profile[0])
# First check for direct conversions, returning immediately if found
direct_converter = self.direct_converters.get((in_str, out_str))
if direct_converter:
out_ts = types_by_format.get(out_str, TypeString(out_str))
return [(direct_converter, TypeString(in_str), out_ts)]
# No direct conversions was found, so find path through graph.
# If profile was plural, add in extra steps.
path = self.dgraph.shortest_path(in_str, out_str)
path += profile[1:]
# Loop through each edge traversal, adding converters and type
# string pairs as we go along. This is to ensure conversion
# profiles that have arguments mid-profile get included.
results = []
for left, right in pair_looper(path):
converter = self.converters.get((_format(left), _format(right)))
right_typestring = types_by_format.get(right, TypeString(right))
results.append((converter, TypeString(left), right_typestring))
return results | python | def find_path(self, in_, out):
'''
Given an input and output TypeString, produce a graph traversal,
keeping in mind special options like Conversion Profiles, Preferred
Paths, and Direct Conversions.
'''
if in_.arguments:
raise ValueError('Cannot originate path in argumented TypeString')
# Determine conversion profile. This is either simply the output, OR,
# if a custom profile has been specified for this output, that custom
# path or type is used.
profile = self.conversion_profiles.get(str(out), str(out))
if isinstance(profile, str):
profile = (profile, )
types_by_format = {_format(s): TypeString(s) for s in profile}
# Normalize input and output types to string
in_str = str(in_)
out_str = _format(profile[0])
# First check for direct conversions, returning immediately if found
direct_converter = self.direct_converters.get((in_str, out_str))
if direct_converter:
out_ts = types_by_format.get(out_str, TypeString(out_str))
return [(direct_converter, TypeString(in_str), out_ts)]
# No direct conversions was found, so find path through graph.
# If profile was plural, add in extra steps.
path = self.dgraph.shortest_path(in_str, out_str)
path += profile[1:]
# Loop through each edge traversal, adding converters and type
# string pairs as we go along. This is to ensure conversion
# profiles that have arguments mid-profile get included.
results = []
for left, right in pair_looper(path):
converter = self.converters.get((_format(left), _format(right)))
right_typestring = types_by_format.get(right, TypeString(right))
results.append((converter, TypeString(left), right_typestring))
return results | [
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michaelpb/omnic | omnic/conversion/graph.py | ConverterGraph.find_path_with_profiles | def find_path_with_profiles(self, conversion_profiles, in_, out):
'''
Like find_path, except forces the conversion profiles to be the given
conversion profile setting. Useful for "temporarily overriding" the
global conversion profiles with your own.
'''
original_profiles = dict(self.conversion_profiles)
self._setup_profiles(conversion_profiles)
results = self.find_path(in_, out)
self.conversion_profiles = original_profiles
return results | python | def find_path_with_profiles(self, conversion_profiles, in_, out):
'''
Like find_path, except forces the conversion profiles to be the given
conversion profile setting. Useful for "temporarily overriding" the
global conversion profiles with your own.
'''
original_profiles = dict(self.conversion_profiles)
self._setup_profiles(conversion_profiles)
results = self.find_path(in_, out)
self.conversion_profiles = original_profiles
return results | [
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dailymuse/oz | oz/error_pages/__init__.py | get_lines_from_file | def get_lines_from_file(filename, lineno, context_lines):
"""
Returns context_lines before and after lineno from file.
Returns (pre_context_lineno, pre_context, context_line, post_context).
"""
def get_lines(start, end):
return [linecache.getline(filename, l).rstrip() for l in range(start, end)]
lower_bound = max(1, lineno - context_lines)
upper_bound = lineno + context_lines
linecache.checkcache(filename)
pre_context = get_lines(lower_bound, lineno)
context_line = linecache.getline(filename, lineno).rstrip()
post_context = get_lines(lineno + 1, upper_bound)
return lower_bound, pre_context, context_line, post_context | python | def get_lines_from_file(filename, lineno, context_lines):
"""
Returns context_lines before and after lineno from file.
Returns (pre_context_lineno, pre_context, context_line, post_context).
"""
def get_lines(start, end):
return [linecache.getline(filename, l).rstrip() for l in range(start, end)]
lower_bound = max(1, lineno - context_lines)
upper_bound = lineno + context_lines
linecache.checkcache(filename)
pre_context = get_lines(lower_bound, lineno)
context_line = linecache.getline(filename, lineno).rstrip()
post_context = get_lines(lineno + 1, upper_bound)
return lower_bound, pre_context, context_line, post_context | [
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dailymuse/oz | oz/error_pages/__init__.py | get_frames | def get_frames(tback, is_breakpoint):
"""Builds a list of ErrorFrame objects from a traceback"""
frames = []
while tback is not None:
if tback.tb_next is None and is_breakpoint:
break
filename = tback.tb_frame.f_code.co_filename
function = tback.tb_frame.f_code.co_name
context = tback.tb_frame.f_locals
lineno = tback.tb_lineno - 1
tback_id = id(tback)
pre_context_lineno, pre_context, context_line, post_context = get_lines_from_file(filename, lineno + 1, 7)
frames.append(ErrorFrame(tback, filename, function, lineno, context, tback_id, pre_context, context_line, post_context, pre_context_lineno))
tback = tback.tb_next
return frames | python | def get_frames(tback, is_breakpoint):
"""Builds a list of ErrorFrame objects from a traceback"""
frames = []
while tback is not None:
if tback.tb_next is None and is_breakpoint:
break
filename = tback.tb_frame.f_code.co_filename
function = tback.tb_frame.f_code.co_name
context = tback.tb_frame.f_locals
lineno = tback.tb_lineno - 1
tback_id = id(tback)
pre_context_lineno, pre_context, context_line, post_context = get_lines_from_file(filename, lineno + 1, 7)
frames.append(ErrorFrame(tback, filename, function, lineno, context, tback_id, pre_context, context_line, post_context, pre_context_lineno))
tback = tback.tb_next
return frames | [
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dailymuse/oz | oz/error_pages/__init__.py | prettify_object | def prettify_object(obj):
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try:
return pprint.pformat(str(obj))
except UnicodeDecodeError as e:
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except Exception as e:
return "[could not display: <%s: %s>]" % (e.__class__.__name__, str(e)) | python | def prettify_object(obj):
"""Makes a pretty string for an object for nice output"""
try:
return pprint.pformat(str(obj))
except UnicodeDecodeError as e:
raise
except Exception as e:
return "[could not display: <%s: %s>]" % (e.__class__.__name__, str(e)) | [
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natea/django-deployer | django_deployer/utils.py | clone_git_repo | def clone_git_repo(repo_url):
"""
input: repo_url
output: path of the cloned repository
steps:
1. clone the repo
2. parse 'site' into for templating
assumptions:
repo_url = "git@github.com:littleq0903/django-deployer-template-openshift-experiment.git"
repo_local_location = "/tmp/djangodeployer-cache-xxxx" # xxxx here will be some short uuid for identify different downloads
"""
REPO_PREFIX = "djangodeployer-cache-"
REPO_POSTFIX_UUID = str(uuid.uuid4()).split('-')[-1]
REPO_CACHE_NAME = REPO_PREFIX + REPO_POSTFIX_UUID
REPO_CACHE_LOCATION = '/tmp/%s' % REPO_CACHE_NAME
repo = git.Repo.clone_from(repo_url, REPO_CACHE_LOCATION)
return REPO_CACHE_LOCATION | python | def clone_git_repo(repo_url):
"""
input: repo_url
output: path of the cloned repository
steps:
1. clone the repo
2. parse 'site' into for templating
assumptions:
repo_url = "git@github.com:littleq0903/django-deployer-template-openshift-experiment.git"
repo_local_location = "/tmp/djangodeployer-cache-xxxx" # xxxx here will be some short uuid for identify different downloads
"""
REPO_PREFIX = "djangodeployer-cache-"
REPO_POSTFIX_UUID = str(uuid.uuid4()).split('-')[-1]
REPO_CACHE_NAME = REPO_PREFIX + REPO_POSTFIX_UUID
REPO_CACHE_LOCATION = '/tmp/%s' % REPO_CACHE_NAME
repo = git.Repo.clone_from(repo_url, REPO_CACHE_LOCATION)
return REPO_CACHE_LOCATION | [
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output: path of the cloned repository
steps:
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2. parse 'site' into for templating
assumptions:
repo_url = "git@github.com:littleq0903/django-deployer-template-openshift-experiment.git"
repo_local_location = "/tmp/djangodeployer-cache-xxxx" # xxxx here will be some short uuid for identify different downloads | [
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natea/django-deployer | django_deployer/utils.py | get_template_filelist | def get_template_filelist(repo_path, ignore_files=[], ignore_folders=[]):
"""
input: local repo path
output: path list of files which need to be rendered
"""
default_ignore_files = ['.gitignore']
default_ignore_folders = ['.git']
ignore_files += default_ignore_files
ignore_folders += default_ignore_folders
filelist = []
for root, folders, files in os.walk(repo_path):
for ignore_file in ignore_files:
if ignore_file in files:
files.remove(ignore_file)
for ignore_folder in ignore_folders:
if ignore_folder in folders:
folders.remove(ignore_folder)
for file_name in files:
filelist.append( '%s/%s' % (root, file_name))
return filelist | python | def get_template_filelist(repo_path, ignore_files=[], ignore_folders=[]):
"""
input: local repo path
output: path list of files which need to be rendered
"""
default_ignore_files = ['.gitignore']
default_ignore_folders = ['.git']
ignore_files += default_ignore_files
ignore_folders += default_ignore_folders
filelist = []
for root, folders, files in os.walk(repo_path):
for ignore_file in ignore_files:
if ignore_file in files:
files.remove(ignore_file)
for ignore_folder in ignore_folders:
if ignore_folder in folders:
folders.remove(ignore_folder)
for file_name in files:
filelist.append( '%s/%s' % (root, file_name))
return filelist | [
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natea/django-deployer | django_deployer/utils.py | render_from_repo | def render_from_repo(repo_path, to_path, template_params, settings_dir):
"""
rendering all files into the target directory
"""
TEMPLATE_PROJECT_FOLDER_PLACEHOLDER_NAME = 'deployer_project'
repo_path = repo_path.rstrip('/')
to_path = to_path.rstrip('/')
files_to_render = get_template_filelist(repo_path, ignore_folders=[TEMPLATE_PROJECT_FOLDER_PLACEHOLDER_NAME])
# rendering generic deploy files
for single_file_path in files_to_render:
source_file_path = single_file_path
dest_file_path = source_file_path.replace(repo_path, to_path)
render_from_single_file(source_file_path, dest_file_path, template_params)
settings_template_dir = os.path.join(repo_path, TEMPLATE_PROJECT_FOLDER_PLACEHOLDER_NAME)
settings_files = get_template_filelist(settings_template_dir)
# rendering settings file
for single_file_path in settings_files:
source = single_file_path
dest = single_file_path.replace(settings_template_dir, settings_dir)
render_from_single_file(source, dest, template_params) | python | def render_from_repo(repo_path, to_path, template_params, settings_dir):
"""
rendering all files into the target directory
"""
TEMPLATE_PROJECT_FOLDER_PLACEHOLDER_NAME = 'deployer_project'
repo_path = repo_path.rstrip('/')
to_path = to_path.rstrip('/')
files_to_render = get_template_filelist(repo_path, ignore_folders=[TEMPLATE_PROJECT_FOLDER_PLACEHOLDER_NAME])
# rendering generic deploy files
for single_file_path in files_to_render:
source_file_path = single_file_path
dest_file_path = source_file_path.replace(repo_path, to_path)
render_from_single_file(source_file_path, dest_file_path, template_params)
settings_template_dir = os.path.join(repo_path, TEMPLATE_PROJECT_FOLDER_PLACEHOLDER_NAME)
settings_files = get_template_filelist(settings_template_dir)
# rendering settings file
for single_file_path in settings_files:
source = single_file_path
dest = single_file_path.replace(settings_template_dir, settings_dir)
render_from_single_file(source, dest, template_params) | [
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9b/frisbee | frisbee/utils.py | gen_logger | def gen_logger(name: str, log_level: int=logging.INFO) -> logging.Logger:
"""Create a logger to be used between processes.
:returns: Logging instance.
"""
logger = logging.getLogger(name)
logger.setLevel(log_level)
shandler: logging.StreamHandler = logging.StreamHandler(sys.stdout)
fmt: str = '\033[1;32m%(levelname)-5s %(module)s:%(funcName)s():'
fmt += '%(lineno)d %(asctime)s\033[0m| %(message)s'
shandler.setFormatter(logging.Formatter(fmt))
logger.addHandler(shandler)
return logger | python | def gen_logger(name: str, log_level: int=logging.INFO) -> logging.Logger:
"""Create a logger to be used between processes.
:returns: Logging instance.
"""
logger = logging.getLogger(name)
logger.setLevel(log_level)
shandler: logging.StreamHandler = logging.StreamHandler(sys.stdout)
fmt: str = '\033[1;32m%(levelname)-5s %(module)s:%(funcName)s():'
fmt += '%(lineno)d %(asctime)s\033[0m| %(message)s'
shandler.setFormatter(logging.Formatter(fmt))
logger.addHandler(shandler)
return logger | [
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9b/frisbee | frisbee/utils.py | gen_headers | def gen_headers() -> Dict[str, str]:
"""Generate a header pairing."""
ua_list: List[str] = ['Mozilla/5.0 (Windows NT 6.3; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/33.0.1750.117 Safari/537.36']
headers: Dict[str, str] = {'User-Agent': ua_list[random.randint(0, len(ua_list) - 1)]}
return headers | python | def gen_headers() -> Dict[str, str]:
"""Generate a header pairing."""
ua_list: List[str] = ['Mozilla/5.0 (Windows NT 6.3; WOW64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/33.0.1750.117 Safari/537.36']
headers: Dict[str, str] = {'User-Agent': ua_list[random.randint(0, len(ua_list) - 1)]}
return headers | [
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9b/frisbee | frisbee/utils.py | extract_emails | def extract_emails(results: str, domain: str, fuzzy: bool) -> List[str]:
"""Grab email addresses from raw text data."""
pattern: Pattern = re.compile(r'([\w.-]+@[\w.-]+)')
hits: List[str] = pattern.findall(results)
if fuzzy:
seed = domain.split('.')[0]
emails: List[str] = [x.lower() for x in hits if x.split('@')[1].__contains__(seed)]
else:
emails: List[str] = [x.lower() for x in hits if x.endswith(domain)]
return list(set(emails)) | python | def extract_emails(results: str, domain: str, fuzzy: bool) -> List[str]:
"""Grab email addresses from raw text data."""
pattern: Pattern = re.compile(r'([\w.-]+@[\w.-]+)')
hits: List[str] = pattern.findall(results)
if fuzzy:
seed = domain.split('.')[0]
emails: List[str] = [x.lower() for x in hits if x.split('@')[1].__contains__(seed)]
else:
emails: List[str] = [x.lower() for x in hits if x.endswith(domain)]
return list(set(emails)) | [
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biocore/burrito-fillings | bfillings/blast.py | seqs_to_stream | def seqs_to_stream(seqs, ih):
"""Converts seqs into stream of FASTA records, depending on input handler.
Each FASTA record will be a list of lines.
"""
if ih == '_input_as_multiline_string':
recs = FastaFinder(seqs.split('\n'))
elif ih == '_input_as_string':
recs = FastaFinder(open(seqs))
elif ih == '_input_as_seqs':
recs = [['>'+str(i), s] for i, s in enumerate(seqs)]
elif ih == '_input_as_lines':
recs = FastaFinder(seqs)
else:
raise TypeError, "Unknown input handler %s" % ih
return recs | python | def seqs_to_stream(seqs, ih):
"""Converts seqs into stream of FASTA records, depending on input handler.
Each FASTA record will be a list of lines.
"""
if ih == '_input_as_multiline_string':
recs = FastaFinder(seqs.split('\n'))
elif ih == '_input_as_string':
recs = FastaFinder(open(seqs))
elif ih == '_input_as_seqs':
recs = [['>'+str(i), s] for i, s in enumerate(seqs)]
elif ih == '_input_as_lines':
recs = FastaFinder(seqs)
else:
raise TypeError, "Unknown input handler %s" % ih
return recs | [
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biocore/burrito-fillings | bfillings/blast.py | blast_seqs | def blast_seqs(seqs,
blast_constructor,
blast_db=None,
blast_mat_root=None,
params={},
add_seq_names=True,
out_filename=None,
WorkingDir=None,
SuppressStderr=None,
SuppressStdout=None,
input_handler=None,
HALT_EXEC=False
):
"""Blast list of sequences.
seqs: either file name or list of sequence objects or list of strings or
single multiline string containing sequences.
WARNING: DECISION RULES FOR INPUT HANDLING HAVE CHANGED. Decision rules
for data are as follows. If it's s list, treat as lines, unless
add_seq_names is true (in which case treat as list of seqs). If it's a
string, test whether it has newlines. If it doesn't have newlines, assume
it's a filename. If it does have newlines, it can't be a filename, so
assume it's a multiline string containing sequences.
If you want to skip the detection and force a specific type of input
handler, use input_handler='your_favorite_handler'.
add_seq_names: boolean. if True, sequence names are inserted in the list
of sequences. if False, it assumes seqs is a list of lines of some
proper format that the program can handle
"""
# set num keep
if blast_db:
params["-d"] = blast_db
if out_filename:
params["-o"] = out_filename
ih = input_handler or guess_input_handler(seqs, add_seq_names)
blast_app = blast_constructor(
params=params,
blast_mat_root=blast_mat_root,
InputHandler=ih,
WorkingDir=WorkingDir,
SuppressStderr=SuppressStderr,
SuppressStdout=SuppressStdout,
HALT_EXEC=HALT_EXEC)
return blast_app(seqs) | python | def blast_seqs(seqs,
blast_constructor,
blast_db=None,
blast_mat_root=None,
params={},
add_seq_names=True,
out_filename=None,
WorkingDir=None,
SuppressStderr=None,
SuppressStdout=None,
input_handler=None,
HALT_EXEC=False
):
"""Blast list of sequences.
seqs: either file name or list of sequence objects or list of strings or
single multiline string containing sequences.
WARNING: DECISION RULES FOR INPUT HANDLING HAVE CHANGED. Decision rules
for data are as follows. If it's s list, treat as lines, unless
add_seq_names is true (in which case treat as list of seqs). If it's a
string, test whether it has newlines. If it doesn't have newlines, assume
it's a filename. If it does have newlines, it can't be a filename, so
assume it's a multiline string containing sequences.
If you want to skip the detection and force a specific type of input
handler, use input_handler='your_favorite_handler'.
add_seq_names: boolean. if True, sequence names are inserted in the list
of sequences. if False, it assumes seqs is a list of lines of some
proper format that the program can handle
"""
# set num keep
if blast_db:
params["-d"] = blast_db
if out_filename:
params["-o"] = out_filename
ih = input_handler or guess_input_handler(seqs, add_seq_names)
blast_app = blast_constructor(
params=params,
blast_mat_root=blast_mat_root,
InputHandler=ih,
WorkingDir=WorkingDir,
SuppressStderr=SuppressStderr,
SuppressStdout=SuppressStdout,
HALT_EXEC=HALT_EXEC)
return blast_app(seqs) | [
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biocore/burrito-fillings | bfillings/blast.py | fasta_cmd_get_seqs | def fasta_cmd_get_seqs(acc_list,
blast_db=None,
is_protein=None,
out_filename=None,
params={},
WorkingDir=tempfile.gettempdir(),
SuppressStderr=None,
SuppressStdout=None):
"""Retrieve sequences for list of accessions """
if is_protein is None:
params["-p"] = 'G'
elif is_protein:
params["-p"] = 'T'
else:
params["-p"] = 'F'
if blast_db:
params["-d"] = blast_db
if out_filename:
params["-o"] = out_filename
# turn off duplicate accessions
params["-a"] = "F"
# create Psi-BLAST
fasta_cmd = FastaCmd(params=params,
InputHandler='_input_as_string',
WorkingDir=WorkingDir,
SuppressStderr=SuppressStderr,
SuppressStdout=SuppressStdout)
# return results
return fasta_cmd("\"%s\"" % ','.join(acc_list)) | python | def fasta_cmd_get_seqs(acc_list,
blast_db=None,
is_protein=None,
out_filename=None,
params={},
WorkingDir=tempfile.gettempdir(),
SuppressStderr=None,
SuppressStdout=None):
"""Retrieve sequences for list of accessions """
if is_protein is None:
params["-p"] = 'G'
elif is_protein:
params["-p"] = 'T'
else:
params["-p"] = 'F'
if blast_db:
params["-d"] = blast_db
if out_filename:
params["-o"] = out_filename
# turn off duplicate accessions
params["-a"] = "F"
# create Psi-BLAST
fasta_cmd = FastaCmd(params=params,
InputHandler='_input_as_string',
WorkingDir=WorkingDir,
SuppressStderr=SuppressStderr,
SuppressStdout=SuppressStdout)
# return results
return fasta_cmd("\"%s\"" % ','.join(acc_list)) | [
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biocore/burrito-fillings | bfillings/blast.py | seqs_from_fastacmd | def seqs_from_fastacmd(acc_list, blast_db,is_protein=True):
"""Get dict of description:seq from fastacmd."""
fasta_cmd_res = fasta_cmd_get_seqs(acc_list, blast_db=blast_db, \
is_protein=is_protein)
recs = FastaCmdFinder(fasta_cmd_res['StdOut'])
result = {}
for rec in recs:
try:
result[rec[0][1:].strip()] = ''.join(map(strip, rec[1:]))
except IndexError: #maybe we didn't get a sequence?
pass
fasta_cmd_res.cleanUp()
return result | python | def seqs_from_fastacmd(acc_list, blast_db,is_protein=True):
"""Get dict of description:seq from fastacmd."""
fasta_cmd_res = fasta_cmd_get_seqs(acc_list, blast_db=blast_db, \
is_protein=is_protein)
recs = FastaCmdFinder(fasta_cmd_res['StdOut'])
result = {}
for rec in recs:
try:
result[rec[0][1:].strip()] = ''.join(map(strip, rec[1:]))
except IndexError: #maybe we didn't get a sequence?
pass
fasta_cmd_res.cleanUp()
return result | [
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biocore/burrito-fillings | bfillings/blast.py | psiblast_n_neighbors | def psiblast_n_neighbors(seqs,
n=100,
blast_db=None,
core_threshold=1e-50,
extra_threshold=1e-10,
lower_threshold=1e-6,
step=100,
method="two-step",
blast_mat_root=None,
params={},
add_seq_names=False,
WorkingDir=None,
SuppressStderr=None,
SuppressStdout=None,
input_handler=None,
scorer=3, #shotgun with 3 hits needed to keep
second_db=None
):
"""PsiBlasts sequences, stopping when n neighbors are reached.
core_threshold: threshold for the core profile (default: 1e-50)
extra_threshold: threshold for pulling in additional seqs (default:1e-10)
lower_threshold: threshold for seqs in final round (default:1e-6)
seqs: either file name or list of sequence objects or list of strings or
single multiline string containing sequences.
If you want to skip the detection and force a specific type of input
handler, use input_handler='your_favorite_handler'.
add_seq_names: boolean. if True, sequence names are inserted in the list
of sequences. if False, it assumes seqs is a list of lines of some
proper format that the program can handle
"""
if blast_db:
params["-d"] = blast_db
ih = input_handler or guess_input_handler(seqs, add_seq_names)
recs = seqs_to_stream(seqs, ih) #checkpointing can only handle one seq...
#set up the parameters for the core and additional runs
max_iterations = params['-j']
params['-j'] = 2 #won't checkpoint with single iteration
app = PsiBlast(params=params,
blast_mat_root=blast_mat_root,
InputHandler='_input_as_lines',
WorkingDir=WorkingDir,
SuppressStderr=SuppressStderr,
SuppressStdout=SuppressStdout,
)
result = {}
for seq in recs:
query_id = seq[0][1:].split(None,1)[0]
if method == "two-step":
result[query_id] = ids_from_seq_two_step(seq, n, max_iterations, \
app, core_threshold, extra_threshold, lower_threshold, second_db)
elif method == "lower_threshold":
result[query_id] = ids_from_seq_lower_threshold(seq, n, \
max_iterations, app, core_threshold, lower_threshold, step)
elif method == "iterative":
result[query_id] = ids_from_seqs_iterative(seq, app, \
QMEPsiBlast9, scorer, params['-j'], n)
else:
raise TypeError, "Got unknown method %s" % method
params['-j'] = max_iterations
return result | python | def psiblast_n_neighbors(seqs,
n=100,
blast_db=None,
core_threshold=1e-50,
extra_threshold=1e-10,
lower_threshold=1e-6,
step=100,
method="two-step",
blast_mat_root=None,
params={},
add_seq_names=False,
WorkingDir=None,
SuppressStderr=None,
SuppressStdout=None,
input_handler=None,
scorer=3, #shotgun with 3 hits needed to keep
second_db=None
):
"""PsiBlasts sequences, stopping when n neighbors are reached.
core_threshold: threshold for the core profile (default: 1e-50)
extra_threshold: threshold for pulling in additional seqs (default:1e-10)
lower_threshold: threshold for seqs in final round (default:1e-6)
seqs: either file name or list of sequence objects or list of strings or
single multiline string containing sequences.
If you want to skip the detection and force a specific type of input
handler, use input_handler='your_favorite_handler'.
add_seq_names: boolean. if True, sequence names are inserted in the list
of sequences. if False, it assumes seqs is a list of lines of some
proper format that the program can handle
"""
if blast_db:
params["-d"] = blast_db
ih = input_handler or guess_input_handler(seqs, add_seq_names)
recs = seqs_to_stream(seqs, ih) #checkpointing can only handle one seq...
#set up the parameters for the core and additional runs
max_iterations = params['-j']
params['-j'] = 2 #won't checkpoint with single iteration
app = PsiBlast(params=params,
blast_mat_root=blast_mat_root,
InputHandler='_input_as_lines',
WorkingDir=WorkingDir,
SuppressStderr=SuppressStderr,
SuppressStdout=SuppressStdout,
)
result = {}
for seq in recs:
query_id = seq[0][1:].split(None,1)[0]
if method == "two-step":
result[query_id] = ids_from_seq_two_step(seq, n, max_iterations, \
app, core_threshold, extra_threshold, lower_threshold, second_db)
elif method == "lower_threshold":
result[query_id] = ids_from_seq_lower_threshold(seq, n, \
max_iterations, app, core_threshold, lower_threshold, step)
elif method == "iterative":
result[query_id] = ids_from_seqs_iterative(seq, app, \
QMEPsiBlast9, scorer, params['-j'], n)
else:
raise TypeError, "Got unknown method %s" % method
params['-j'] = max_iterations
return result | [
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core_threshold: threshold for the core profile (default: 1e-50)
extra_threshold: threshold for pulling in additional seqs (default:1e-10)
lower_threshold: threshold for seqs in final round (default:1e-6)
seqs: either file name or list of sequence objects or list of strings or
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add_seq_names: boolean. if True, sequence names are inserted in the list
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biocore/burrito-fillings | bfillings/blast.py | ids_from_seq_two_step | def ids_from_seq_two_step(seq, n, max_iterations, app, core_threshold, \
extra_threshold, lower_threshold, second_db=None):
"""Returns ids that match a seq, using a 2-tiered strategy.
Optionally uses a second database for the second search.
"""
#first time through: reset 'h' and 'e' to core
#-h is the e-value threshold for including seqs in the score matrix model
app.Parameters['-h'].on(core_threshold)
#-e is the e-value threshold for the final blast
app.Parameters['-e'].on(core_threshold)
checkpoints = []
ids = []
last_num_ids = None
for i in range(max_iterations):
if checkpoints:
app.Parameters['-R'].on(checkpoints[-1])
curr_check = 'checkpoint_%s.chk' % i
app.Parameters['-C'].on(curr_check)
output = app(seq)
#if we didn't write a checkpoint, bail out
if not access(curr_check, F_OK):
break
#if we got here, we wrote a checkpoint file
checkpoints.append(curr_check)
result = list(output.get('BlastOut', output['StdOut']))
output.cleanUp()
if result:
ids = LastProteinIds9(result,keep_values=True,filter_identity=False)
num_ids = len(ids)
if num_ids >= n:
break
if num_ids == last_num_ids:
break
last_num_ids = num_ids
#if we didn't write any checkpoints, second run won't work, so return ids
if not checkpoints:
return ids
#if we got too many ids and don't have a second database, return the ids we got
if (not second_db) and num_ids >= n:
return ids
#second time through: reset 'h' and 'e' to get extra hits, and switch the
#database if appropriate
app.Parameters['-h'].on(extra_threshold)
app.Parameters['-e'].on(lower_threshold)
if second_db:
app.Parameters['-d'].on(second_db)
for i in range(max_iterations): #will always have last_check if we get here
app.Parameters['-R'].on(checkpoints[-1])
curr_check = 'checkpoint_b_%s.chk' % i
app.Parameters['-C'].on(curr_check)
output = app(seq)
#bail out if we couldn't write a checkpoint
if not access(curr_check, F_OK):
break
#if we got here, the checkpoint worked
checkpoints.append(curr_check)
result = list(output.get('BlastOut', output['StdOut']))
if result:
ids = LastProteinIds9(result,keep_values=True,filter_identity=False)
num_ids = len(ids)
if num_ids >= n:
break
if num_ids == last_num_ids:
break
last_num_ids = num_ids
#return the ids we got. may not be as many as we wanted.
for c in checkpoints:
remove(c)
return ids | python | def ids_from_seq_two_step(seq, n, max_iterations, app, core_threshold, \
extra_threshold, lower_threshold, second_db=None):
"""Returns ids that match a seq, using a 2-tiered strategy.
Optionally uses a second database for the second search.
"""
#first time through: reset 'h' and 'e' to core
#-h is the e-value threshold for including seqs in the score matrix model
app.Parameters['-h'].on(core_threshold)
#-e is the e-value threshold for the final blast
app.Parameters['-e'].on(core_threshold)
checkpoints = []
ids = []
last_num_ids = None
for i in range(max_iterations):
if checkpoints:
app.Parameters['-R'].on(checkpoints[-1])
curr_check = 'checkpoint_%s.chk' % i
app.Parameters['-C'].on(curr_check)
output = app(seq)
#if we didn't write a checkpoint, bail out
if not access(curr_check, F_OK):
break
#if we got here, we wrote a checkpoint file
checkpoints.append(curr_check)
result = list(output.get('BlastOut', output['StdOut']))
output.cleanUp()
if result:
ids = LastProteinIds9(result,keep_values=True,filter_identity=False)
num_ids = len(ids)
if num_ids >= n:
break
if num_ids == last_num_ids:
break
last_num_ids = num_ids
#if we didn't write any checkpoints, second run won't work, so return ids
if not checkpoints:
return ids
#if we got too many ids and don't have a second database, return the ids we got
if (not second_db) and num_ids >= n:
return ids
#second time through: reset 'h' and 'e' to get extra hits, and switch the
#database if appropriate
app.Parameters['-h'].on(extra_threshold)
app.Parameters['-e'].on(lower_threshold)
if second_db:
app.Parameters['-d'].on(second_db)
for i in range(max_iterations): #will always have last_check if we get here
app.Parameters['-R'].on(checkpoints[-1])
curr_check = 'checkpoint_b_%s.chk' % i
app.Parameters['-C'].on(curr_check)
output = app(seq)
#bail out if we couldn't write a checkpoint
if not access(curr_check, F_OK):
break
#if we got here, the checkpoint worked
checkpoints.append(curr_check)
result = list(output.get('BlastOut', output['StdOut']))
if result:
ids = LastProteinIds9(result,keep_values=True,filter_identity=False)
num_ids = len(ids)
if num_ids >= n:
break
if num_ids == last_num_ids:
break
last_num_ids = num_ids
#return the ids we got. may not be as many as we wanted.
for c in checkpoints:
remove(c)
return ids | [
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biocore/burrito-fillings | bfillings/blast.py | ids_from_seq_lower_threshold | def ids_from_seq_lower_threshold(seq, n, max_iterations, app, core_threshold, \
lower_threshold, step=100):
"""Returns ids that match a seq, decreasing the sensitivity."""
last_num_ids = None
checkpoints = []
cp_name_base = make_unique_str()
# cache ides for each iteration
# store { iteration_num:(core_threshold, [list of matching ids]) }
all_ids = {}
try:
i=0
while 1:
#-h is the e-value threshold for inclusion in the score matrix model
app.Parameters['-h'].on(core_threshold)
app.Parameters['-e'].on(core_threshold)
if core_threshold > lower_threshold:
raise ThresholdFound
if checkpoints:
#-R restarts from a previously stored file
app.Parameters['-R'].on(checkpoints[-1])
#store the score model from this iteration
curr_check = 'checkpoint_' + cp_name_base + '_' + str(i) + \
'.chk'
app.Parameters['-C'].on(curr_check)
output = app(seq)
result = list(output.get('BlastOut', output['StdOut']))
#sometimes fails on first try -- don't know why, but this seems
#to fix problem
while not result:
output = app(seq)
result = list(output.get('BlastOut', output['StdOut']))
ids = LastProteinIds9(result,keep_values=True,filter_identity=False)
output.cleanUp()
all_ids[i + 1] = (core_threshold, copy(ids))
if not access(curr_check, F_OK):
raise ThresholdFound
checkpoints.append(curr_check)
num_ids = len(ids)
if num_ids >= n:
raise ThresholdFound
last_num_ids = num_ids
core_threshold *= step
if i >= max_iterations - 1: #because max_iterations is 1-based
raise ThresholdFound
i += 1
except ThresholdFound:
for c in checkpoints:
remove(c)
#turn app.Parameters['-R'] off so that for the next file it does not
#try and read in a checkpoint file that is not there
app.Parameters['-R'].off()
return ids, i + 1, all_ids | python | def ids_from_seq_lower_threshold(seq, n, max_iterations, app, core_threshold, \
lower_threshold, step=100):
"""Returns ids that match a seq, decreasing the sensitivity."""
last_num_ids = None
checkpoints = []
cp_name_base = make_unique_str()
# cache ides for each iteration
# store { iteration_num:(core_threshold, [list of matching ids]) }
all_ids = {}
try:
i=0
while 1:
#-h is the e-value threshold for inclusion in the score matrix model
app.Parameters['-h'].on(core_threshold)
app.Parameters['-e'].on(core_threshold)
if core_threshold > lower_threshold:
raise ThresholdFound
if checkpoints:
#-R restarts from a previously stored file
app.Parameters['-R'].on(checkpoints[-1])
#store the score model from this iteration
curr_check = 'checkpoint_' + cp_name_base + '_' + str(i) + \
'.chk'
app.Parameters['-C'].on(curr_check)
output = app(seq)
result = list(output.get('BlastOut', output['StdOut']))
#sometimes fails on first try -- don't know why, but this seems
#to fix problem
while not result:
output = app(seq)
result = list(output.get('BlastOut', output['StdOut']))
ids = LastProteinIds9(result,keep_values=True,filter_identity=False)
output.cleanUp()
all_ids[i + 1] = (core_threshold, copy(ids))
if not access(curr_check, F_OK):
raise ThresholdFound
checkpoints.append(curr_check)
num_ids = len(ids)
if num_ids >= n:
raise ThresholdFound
last_num_ids = num_ids
core_threshold *= step
if i >= max_iterations - 1: #because max_iterations is 1-based
raise ThresholdFound
i += 1
except ThresholdFound:
for c in checkpoints:
remove(c)
#turn app.Parameters['-R'] off so that for the next file it does not
#try and read in a checkpoint file that is not there
app.Parameters['-R'].off()
return ids, i + 1, all_ids | [
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biocore/burrito-fillings | bfillings/blast.py | make_unique_str | def make_unique_str(num_chars=20):
"""make a random string of characters for a temp filename"""
chars = 'abcdefghigklmnopqrstuvwxyz'
all_chars = chars + chars.upper() + '01234567890'
picks = list(all_chars)
return ''.join([choice(picks) for i in range(num_chars)]) | python | def make_unique_str(num_chars=20):
"""make a random string of characters for a temp filename"""
chars = 'abcdefghigklmnopqrstuvwxyz'
all_chars = chars + chars.upper() + '01234567890'
picks = list(all_chars)
return ''.join([choice(picks) for i in range(num_chars)]) | [
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biocore/burrito-fillings | bfillings/blast.py | keep_everything_scorer | def keep_everything_scorer(checked_ids):
"""Returns every query and every match in checked_ids, with best score."""
result = checked_ids.keys()
for i in checked_ids.values():
result.extend(i.keys())
return dict.fromkeys(result).keys() | python | def keep_everything_scorer(checked_ids):
"""Returns every query and every match in checked_ids, with best score."""
result = checked_ids.keys()
for i in checked_ids.values():
result.extend(i.keys())
return dict.fromkeys(result).keys() | [
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biocore/burrito-fillings | bfillings/blast.py | ids_from_seqs_iterative | def ids_from_seqs_iterative(seqs, app, query_parser, \
scorer=keep_everything_scorer, max_iterations=None, blast_db=None,\
max_seqs=None, ):
"""Gets the ids from each seq, then does each additional id until all done.
If scorer is passed in as an int, uses shotgun scorer with that # hits.
"""
if isinstance(scorer, int):
scorer = make_shotgun_scorer(scorer)
seqs_to_check = list(seqs)
checked_ids = {}
curr_iteration = 0
while seqs_to_check:
unchecked_ids = {}
#pass seqs to command
all_output = app(seqs_to_check)
output = all_output.get('BlastOut', all_output['StdOut'])
for query_id, match_id, match_score in query_parser(output):
if query_id not in checked_ids:
checked_ids[query_id] = {}
checked_ids[query_id][match_id] = match_score
if match_id not in checked_ids:
unchecked_ids[match_id] = True
all_output.cleanUp()
if unchecked_ids:
seq_file = fasta_cmd_get_seqs(unchecked_ids.keys(),
app.Parameters['-d'].Value)['StdOut']
seqs_to_check = []
for s in FastaCmdFinder(fasta_cmd_get_seqs(\
unchecked_ids.keys(), app.Parameters['-d'].Value)['StdOut']):
seqs_to_check.extend(s)
else:
seqs_to_check = []
#bail out if max iterations or max seqs was defined and we've reached it
curr_iteration += 1
if max_iterations and (curr_iteration >= max_iterations):
break
if max_seqs:
curr = scorer(checked_ids)
if len(curr) >= max_seqs:
return curr
return scorer(checked_ids) | python | def ids_from_seqs_iterative(seqs, app, query_parser, \
scorer=keep_everything_scorer, max_iterations=None, blast_db=None,\
max_seqs=None, ):
"""Gets the ids from each seq, then does each additional id until all done.
If scorer is passed in as an int, uses shotgun scorer with that # hits.
"""
if isinstance(scorer, int):
scorer = make_shotgun_scorer(scorer)
seqs_to_check = list(seqs)
checked_ids = {}
curr_iteration = 0
while seqs_to_check:
unchecked_ids = {}
#pass seqs to command
all_output = app(seqs_to_check)
output = all_output.get('BlastOut', all_output['StdOut'])
for query_id, match_id, match_score in query_parser(output):
if query_id not in checked_ids:
checked_ids[query_id] = {}
checked_ids[query_id][match_id] = match_score
if match_id not in checked_ids:
unchecked_ids[match_id] = True
all_output.cleanUp()
if unchecked_ids:
seq_file = fasta_cmd_get_seqs(unchecked_ids.keys(),
app.Parameters['-d'].Value)['StdOut']
seqs_to_check = []
for s in FastaCmdFinder(fasta_cmd_get_seqs(\
unchecked_ids.keys(), app.Parameters['-d'].Value)['StdOut']):
seqs_to_check.extend(s)
else:
seqs_to_check = []
#bail out if max iterations or max seqs was defined and we've reached it
curr_iteration += 1
if max_iterations and (curr_iteration >= max_iterations):
break
if max_seqs:
curr = scorer(checked_ids)
if len(curr) >= max_seqs:
return curr
return scorer(checked_ids) | [
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biocore/burrito-fillings | bfillings/blast.py | blastp | def blastp(seqs, blast_db="nr", e_value="1e-20", max_hits=200,
working_dir=tempfile.gettempdir(), blast_mat_root=None,
extra_params={}):
"""
Returns BlastResult from input seqs, using blastp.
Need to add doc string
"""
# set up params to use with blastp
params = {
# matrix
"-M":"BLOSUM62",
# max procs
"-a":"1",
# expectation
"-e":e_value,
# max seqs to show
"-b":max_hits,
# max one line descriptions
"-v":max_hits,
# program
"-p":"blastp"
}
params.update(extra_params)
# blast
blast_res = blast_seqs(seqs,
Blastall,
blast_mat_root=blast_mat_root,
blast_db=blast_db,
params=params,
add_seq_names=False,
WorkingDir=working_dir
)
# get prot id map
if blast_res['StdOut']:
lines = [x for x in blast_res['StdOut']]
return BlastResult(lines)
return None | python | def blastp(seqs, blast_db="nr", e_value="1e-20", max_hits=200,
working_dir=tempfile.gettempdir(), blast_mat_root=None,
extra_params={}):
"""
Returns BlastResult from input seqs, using blastp.
Need to add doc string
"""
# set up params to use with blastp
params = {
# matrix
"-M":"BLOSUM62",
# max procs
"-a":"1",
# expectation
"-e":e_value,
# max seqs to show
"-b":max_hits,
# max one line descriptions
"-v":max_hits,
# program
"-p":"blastp"
}
params.update(extra_params)
# blast
blast_res = blast_seqs(seqs,
Blastall,
blast_mat_root=blast_mat_root,
blast_db=blast_db,
params=params,
add_seq_names=False,
WorkingDir=working_dir
)
# get prot id map
if blast_res['StdOut']:
lines = [x for x in blast_res['StdOut']]
return BlastResult(lines)
return None | [
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lorien/runscript | runscript/lock.py | set_lock | def set_lock(fname):
"""
Try to lock file and write PID.
Return the status of operation.
"""
global fh
fh = open(fname, 'w')
if os.name == 'nt':
# Code for NT systems got from: http://code.activestate.com/recipes/65203/
import win32con
import win32file
import pywintypes
LOCK_EX = win32con.LOCKFILE_EXCLUSIVE_LOCK
LOCK_SH = 0 # the default
LOCK_NB = win32con.LOCKFILE_FAIL_IMMEDIATELY
# is there any reason not to reuse the following structure?
__overlapped = pywintypes.OVERLAPPED()
hfile = win32file._get_osfhandle(fh.fileno())
try:
win32file.LockFileEx(hfile, LOCK_EX | LOCK_NB, 0, -0x10000, __overlapped)
except pywintypes.error as exc_value:
# error: (33, 'LockFileEx', 'The process cannot access
# the file because another process has locked a portion
# of the file.')
if exc_value[0] == 33:
return False
else:
from fcntl import flock, LOCK_EX, LOCK_NB
try:
flock(fh.fileno(), LOCK_EX | LOCK_NB)
except Exception as ex:
return False
fh.write(str(os.getpid()))
fh.flush()
return True | python | def set_lock(fname):
"""
Try to lock file and write PID.
Return the status of operation.
"""
global fh
fh = open(fname, 'w')
if os.name == 'nt':
# Code for NT systems got from: http://code.activestate.com/recipes/65203/
import win32con
import win32file
import pywintypes
LOCK_EX = win32con.LOCKFILE_EXCLUSIVE_LOCK
LOCK_SH = 0 # the default
LOCK_NB = win32con.LOCKFILE_FAIL_IMMEDIATELY
# is there any reason not to reuse the following structure?
__overlapped = pywintypes.OVERLAPPED()
hfile = win32file._get_osfhandle(fh.fileno())
try:
win32file.LockFileEx(hfile, LOCK_EX | LOCK_NB, 0, -0x10000, __overlapped)
except pywintypes.error as exc_value:
# error: (33, 'LockFileEx', 'The process cannot access
# the file because another process has locked a portion
# of the file.')
if exc_value[0] == 33:
return False
else:
from fcntl import flock, LOCK_EX, LOCK_NB
try:
flock(fh.fileno(), LOCK_EX | LOCK_NB)
except Exception as ex:
return False
fh.write(str(os.getpid()))
fh.flush()
return True | [
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lorien/runscript | runscript/lock.py | assert_lock | def assert_lock(fname):
"""
If file is locked then terminate program else lock file.
"""
if not set_lock(fname):
logger.error('File {} is already locked. Terminating.'.format(fname))
sys.exit() | python | def assert_lock(fname):
"""
If file is locked then terminate program else lock file.
"""
if not set_lock(fname):
logger.error('File {} is already locked. Terminating.'.format(fname))
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biocore/burrito-fillings | bfillings/formatdb.py | build_blast_db_from_fasta_path | def build_blast_db_from_fasta_path(fasta_path, is_protein=False,
output_dir=None, HALT_EXEC=False):
"""Build blast db from fasta_path; return db name and list of files created
**If using to create temporary blast databases, you can call
cogent.util.misc.remove_files(db_filepaths) to clean up all the
files created by formatdb when you're done with the database.
fasta_path: path to fasta file of sequences to build database from
is_protein: True if working on protein seqs (default: False)
output_dir: directory where output should be written
(default: directory containing fasta_path)
HALT_EXEC: halt just before running the formatdb command and
print the command -- useful for debugging
"""
fasta_dir, fasta_filename = split(fasta_path)
if not output_dir:
output_dir = fasta_dir or '.'
# Will cd to this directory, so just pass the filename
# so the app is not confused by relative paths
fasta_path = fasta_filename
if not output_dir.endswith('/'):
db_name = output_dir + '/' + fasta_filename
else:
db_name = output_dir + fasta_filename
# instantiate the object
fdb = FormatDb(WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)
if is_protein:
fdb.Parameters['-p'].on('T')
else:
fdb.Parameters['-p'].on('F')
app_result = fdb(fasta_path)
db_filepaths = []
for v in app_result.values():
try:
db_filepaths.append(v.name)
except AttributeError:
# not a file object, so no path to return
pass
return db_name, db_filepaths | python | def build_blast_db_from_fasta_path(fasta_path, is_protein=False,
output_dir=None, HALT_EXEC=False):
"""Build blast db from fasta_path; return db name and list of files created
**If using to create temporary blast databases, you can call
cogent.util.misc.remove_files(db_filepaths) to clean up all the
files created by formatdb when you're done with the database.
fasta_path: path to fasta file of sequences to build database from
is_protein: True if working on protein seqs (default: False)
output_dir: directory where output should be written
(default: directory containing fasta_path)
HALT_EXEC: halt just before running the formatdb command and
print the command -- useful for debugging
"""
fasta_dir, fasta_filename = split(fasta_path)
if not output_dir:
output_dir = fasta_dir or '.'
# Will cd to this directory, so just pass the filename
# so the app is not confused by relative paths
fasta_path = fasta_filename
if not output_dir.endswith('/'):
db_name = output_dir + '/' + fasta_filename
else:
db_name = output_dir + fasta_filename
# instantiate the object
fdb = FormatDb(WorkingDir=output_dir, HALT_EXEC=HALT_EXEC)
if is_protein:
fdb.Parameters['-p'].on('T')
else:
fdb.Parameters['-p'].on('F')
app_result = fdb(fasta_path)
db_filepaths = []
for v in app_result.values():
try:
db_filepaths.append(v.name)
except AttributeError:
# not a file object, so no path to return
pass
return db_name, db_filepaths | [
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biocore/burrito-fillings | bfillings/formatdb.py | build_blast_db_from_fasta_file | def build_blast_db_from_fasta_file(fasta_file, is_protein=False,
output_dir=None, HALT_EXEC=False):
"""Build blast db from fasta_path; return db name and list of files created
**If using to create temporary blast databases, you can call
cogent.util.misc.remove_files(db_filepaths) to clean up all the
files created by formatdb when you're done with the database.
fasta_path: path to fasta file of sequences to build database from
is_protein: True if working on protein seqs (default: False)
output_dir: directory where output should be written
(default: directory containing fasta_path)
HALT_EXEC: halt just before running the formatdb command and
print the command -- useful for debugging
"""
output_dir = output_dir or '.'
_, fasta_path = mkstemp(dir=output_dir, prefix="BLAST_temp_db_",
suffix=".fasta")
fasta_f = open(fasta_path, 'w')
for line in fasta_file:
fasta_f.write('%s\n' % line.strip())
fasta_f.close()
blast_db, db_filepaths = build_blast_db_from_fasta_path(fasta_path,
is_protein=is_protein,
output_dir=None,
HALT_EXEC=HALT_EXEC
)
db_filepaths.append(fasta_path)
return blast_db, db_filepaths | python | def build_blast_db_from_fasta_file(fasta_file, is_protein=False,
output_dir=None, HALT_EXEC=False):
"""Build blast db from fasta_path; return db name and list of files created
**If using to create temporary blast databases, you can call
cogent.util.misc.remove_files(db_filepaths) to clean up all the
files created by formatdb when you're done with the database.
fasta_path: path to fasta file of sequences to build database from
is_protein: True if working on protein seqs (default: False)
output_dir: directory where output should be written
(default: directory containing fasta_path)
HALT_EXEC: halt just before running the formatdb command and
print the command -- useful for debugging
"""
output_dir = output_dir or '.'
_, fasta_path = mkstemp(dir=output_dir, prefix="BLAST_temp_db_",
suffix=".fasta")
fasta_f = open(fasta_path, 'w')
for line in fasta_file:
fasta_f.write('%s\n' % line.strip())
fasta_f.close()
blast_db, db_filepaths = build_blast_db_from_fasta_path(fasta_path,
is_protein=is_protein,
output_dir=None,
HALT_EXEC=HALT_EXEC
)
db_filepaths.append(fasta_path)
return blast_db, db_filepaths | [
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biocore/burrito-fillings | bfillings/formatdb.py | build_blast_db_from_seqs | def build_blast_db_from_seqs(seqs, is_protein=False, output_dir='./',
HALT_EXEC=False):
"""Build blast db from seqs; return db name and list of files created
**If using to create temporary blast databases, you can call
cogent.util.misc.remove_files(db_filepaths) to clean up all the
files created by formatdb when you're done with the database.
seqs: sequence collection or alignment object
is_protein: True if working on protein seqs (default: False)
output_dir: directory where output should be written
(default: current directory)
HALT_EXEC: halt just before running the formatdb command and
print the command -- useful for debugging
"""
# Build a temp filepath
_, tmp_fasta_filepath = mkstemp(prefix='Blast_tmp_db', suffix='.fasta')
# open the temp file
tmp_fasta_file = open(tmp_fasta_filepath, 'w')
# write the sequence collection to file
tmp_fasta_file.write(seqs.toFasta())
tmp_fasta_file.close()
# build the bast database
db_name, db_filepaths = build_blast_db_from_fasta_path(tmp_fasta_filepath,
is_protein=is_protein,
output_dir=output_dir,
HALT_EXEC=HALT_EXEC)
# clean-up the temporary file
remove(tmp_fasta_filepath)
# return the results
return db_name, db_filepaths | python | def build_blast_db_from_seqs(seqs, is_protein=False, output_dir='./',
HALT_EXEC=False):
"""Build blast db from seqs; return db name and list of files created
**If using to create temporary blast databases, you can call
cogent.util.misc.remove_files(db_filepaths) to clean up all the
files created by formatdb when you're done with the database.
seqs: sequence collection or alignment object
is_protein: True if working on protein seqs (default: False)
output_dir: directory where output should be written
(default: current directory)
HALT_EXEC: halt just before running the formatdb command and
print the command -- useful for debugging
"""
# Build a temp filepath
_, tmp_fasta_filepath = mkstemp(prefix='Blast_tmp_db', suffix='.fasta')
# open the temp file
tmp_fasta_file = open(tmp_fasta_filepath, 'w')
# write the sequence collection to file
tmp_fasta_file.write(seqs.toFasta())
tmp_fasta_file.close()
# build the bast database
db_name, db_filepaths = build_blast_db_from_fasta_path(tmp_fasta_filepath,
is_protein=is_protein,
output_dir=output_dir,
HALT_EXEC=HALT_EXEC)
# clean-up the temporary file
remove(tmp_fasta_filepath)
# return the results
return db_name, db_filepaths | [
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biocore/burrito-fillings | bfillings/formatdb.py | parse_command_line_parameters | def parse_command_line_parameters():
""" Parses command line arguments """
usage = 'usage: %prog [options] fasta_filepath'
version = 'Version: %prog 0.1'
parser = OptionParser(usage=usage, version=version)
# A binary 'verbose' flag
parser.add_option('-p', '--is_protein', action='store_true',
dest='is_protein', default=False,
help='Pass if building db of protein sequences [default:'
' False, nucleotide db]')
parser.add_option('-o', '--output_dir', action='store', type='string',
dest='output_dir', default=None,
help='the output directory [default: directory '
'containing input fasta_filepath]')
opts, args = parser.parse_args()
num_args = 1
if len(args) != num_args:
parser.error('Must provide single filepath to build database from.')
return opts, args | python | def parse_command_line_parameters():
""" Parses command line arguments """
usage = 'usage: %prog [options] fasta_filepath'
version = 'Version: %prog 0.1'
parser = OptionParser(usage=usage, version=version)
# A binary 'verbose' flag
parser.add_option('-p', '--is_protein', action='store_true',
dest='is_protein', default=False,
help='Pass if building db of protein sequences [default:'
' False, nucleotide db]')
parser.add_option('-o', '--output_dir', action='store', type='string',
dest='output_dir', default=None,
help='the output directory [default: directory '
'containing input fasta_filepath]')
opts, args = parser.parse_args()
num_args = 1
if len(args) != num_args:
parser.error('Must provide single filepath to build database from.')
return opts, args | [
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biocore/burrito-fillings | bfillings/formatdb.py | FormatDb._input_as_parameter | def _input_as_parameter(self, data):
""" Set the input path and log path based on data (a fasta filepath)
"""
self.Parameters['-i'].on(data)
# access data through self.Parameters so we know it's been cast
# to a FilePath
input_filepath = self.Parameters['-i'].Value
input_file_dir, input_filename = split(input_filepath)
input_file_base, input_file_ext = splitext(input_filename)
# FIXME: the following all other options
# formatdb ignores the working directory if not name is passed.
self.Parameters['-l'].on(FilePath('%s.log') % input_filename)
self.Parameters['-n'].on(FilePath(input_filename))
return '' | python | def _input_as_parameter(self, data):
""" Set the input path and log path based on data (a fasta filepath)
"""
self.Parameters['-i'].on(data)
# access data through self.Parameters so we know it's been cast
# to a FilePath
input_filepath = self.Parameters['-i'].Value
input_file_dir, input_filename = split(input_filepath)
input_file_base, input_file_ext = splitext(input_filename)
# FIXME: the following all other options
# formatdb ignores the working directory if not name is passed.
self.Parameters['-l'].on(FilePath('%s.log') % input_filename)
self.Parameters['-n'].on(FilePath(input_filename))
return '' | [
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biocore/burrito-fillings | bfillings/formatdb.py | FormatDb._get_result_paths | def _get_result_paths(self, data):
""" Build the dict of result filepaths
"""
# access data through self.Parameters so we know it's been cast
# to a FilePath
wd = self.WorkingDir
db_name = self.Parameters['-n'].Value
log_name = self.Parameters['-l'].Value
result = {}
result['log'] = ResultPath(Path=wd + log_name, IsWritten=True)
if self.Parameters['-p'].Value == 'F':
extensions = ['nhr', 'nin', 'nsq', 'nsd', 'nsi']
else:
extensions = ['phr', 'pin', 'psq', 'psd', 'psi']
for extension in extensions:
for file_path in glob(wd + (db_name + '*' + extension)):
# this will match e.g. nr.01.psd and nr.psd
key = file_path.split(db_name + '.')[1]
result_path = ResultPath(Path=file_path, IsWritten=True)
result[key] = result_path
return result | python | def _get_result_paths(self, data):
""" Build the dict of result filepaths
"""
# access data through self.Parameters so we know it's been cast
# to a FilePath
wd = self.WorkingDir
db_name = self.Parameters['-n'].Value
log_name = self.Parameters['-l'].Value
result = {}
result['log'] = ResultPath(Path=wd + log_name, IsWritten=True)
if self.Parameters['-p'].Value == 'F':
extensions = ['nhr', 'nin', 'nsq', 'nsd', 'nsi']
else:
extensions = ['phr', 'pin', 'psq', 'psd', 'psi']
for extension in extensions:
for file_path in glob(wd + (db_name + '*' + extension)):
# this will match e.g. nr.01.psd and nr.psd
key = file_path.split(db_name + '.')[1]
result_path = ResultPath(Path=file_path, IsWritten=True)
result[key] = result_path
return result | [
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dailymuse/oz | oz/redis_sessions/middleware.py | RedisSessionMiddleware._session_key | def _session_key(self):
"""Gets the redis key for a session"""
if not hasattr(self, "_cached_session_key"):
session_id_bytes = self.get_secure_cookie("session_id")
session_id = None
if session_id_bytes:
try:
session_id = session_id_bytes.decode('utf-8')
except:
pass
if not session_id:
session_id = oz.redis_sessions.random_hex(20)
session_time = oz.settings["session_time"]
kwargs = dict(
name="session_id",
value=session_id.encode('utf-8'),
domain=oz.settings.get("cookie_domain"),
httponly=True,
)
if session_time:
kwargs["expires_days"] = round(session_time/60/60/24)
self.set_secure_cookie(**kwargs)
password_salt = oz.settings["session_salt"]
self._cached_session_key = "session:%s:v4" % oz.redis_sessions.password_hash(session_id, password_salt=password_salt)
return self._cached_session_key | python | def _session_key(self):
"""Gets the redis key for a session"""
if not hasattr(self, "_cached_session_key"):
session_id_bytes = self.get_secure_cookie("session_id")
session_id = None
if session_id_bytes:
try:
session_id = session_id_bytes.decode('utf-8')
except:
pass
if not session_id:
session_id = oz.redis_sessions.random_hex(20)
session_time = oz.settings["session_time"]
kwargs = dict(
name="session_id",
value=session_id.encode('utf-8'),
domain=oz.settings.get("cookie_domain"),
httponly=True,
)
if session_time:
kwargs["expires_days"] = round(session_time/60/60/24)
self.set_secure_cookie(**kwargs)
password_salt = oz.settings["session_salt"]
self._cached_session_key = "session:%s:v4" % oz.redis_sessions.password_hash(session_id, password_salt=password_salt)
return self._cached_session_key | [
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dailymuse/oz | oz/redis_sessions/middleware.py | RedisSessionMiddleware._update_session_expiration | def _update_session_expiration(self):
"""
Updates a redis item to expire later since it has been interacted with
recently
"""
session_time = oz.settings["session_time"]
if session_time:
self.redis().expire(self._session_key, session_time) | python | def _update_session_expiration(self):
"""
Updates a redis item to expire later since it has been interacted with
recently
"""
session_time = oz.settings["session_time"]
if session_time:
self.redis().expire(self._session_key, session_time) | [
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dailymuse/oz | oz/redis_sessions/middleware.py | RedisSessionMiddleware.get_session_value | def get_session_value(self, name, default=None):
"""Gets a session value"""
value = self.redis().hget(self._session_key, name) or default
self._update_session_expiration()
return value | python | def get_session_value(self, name, default=None):
"""Gets a session value"""
value = self.redis().hget(self._session_key, name) or default
self._update_session_expiration()
return value | [
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dailymuse/oz | oz/redis_sessions/middleware.py | RedisSessionMiddleware.set_session_value | def set_session_value(self, name, value):
"""Sets a session value"""
self.redis().hset(self._session_key, name, value)
self._update_session_expiration() | python | def set_session_value(self, name, value):
"""Sets a session value"""
self.redis().hset(self._session_key, name, value)
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dailymuse/oz | oz/redis_sessions/middleware.py | RedisSessionMiddleware.clear_session_value | def clear_session_value(self, name):
"""Removes a session value"""
self.redis().hdel(self._session_key, name)
self._update_session_expiration() | python | def clear_session_value(self, name):
"""Removes a session value"""
self.redis().hdel(self._session_key, name)
self._update_session_expiration() | [
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michaelpb/omnic | omnic/web/security.py | rewrite_middleware | async def rewrite_middleware(server, request):
'''
Sanic middleware that utilizes a security class's "rewrite" method to
check
'''
if singletons.settings.SECURITY is not None:
security_class = singletons.settings.load('SECURITY')
else:
security_class = DummySecurity
security = security_class()
try:
new_path = await security.rewrite(request)
except SecurityException as e:
msg = ''
if DEBUG:
msg = str(e)
return server.response.text(msg, status=400)
request.path = new_path | python | async def rewrite_middleware(server, request):
'''
Sanic middleware that utilizes a security class's "rewrite" method to
check
'''
if singletons.settings.SECURITY is not None:
security_class = singletons.settings.load('SECURITY')
else:
security_class = DummySecurity
security = security_class()
try:
new_path = await security.rewrite(request)
except SecurityException as e:
msg = ''
if DEBUG:
msg = str(e)
return server.response.text(msg, status=400)
request.path = new_path | [
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mickybart/python-atlasapi | atlasapi/network.py | Network.answer | def answer(self, c, details):
"""Answer will provide all necessary feedback for the caller
Args:
c (int): HTTP Code
details (dict): Response payload
Returns:
dict: Response payload
Raises:
ErrAtlasBadRequest
ErrAtlasUnauthorized
ErrAtlasForbidden
ErrAtlasNotFound
ErrAtlasMethodNotAllowed
ErrAtlasConflict
ErrAtlasServerErrors
"""
if c in [Settings.SUCCESS, Settings.CREATED, Settings.ACCEPTED]:
return details
elif c == Settings.BAD_REQUEST:
raise ErrAtlasBadRequest(c, details)
elif c == Settings.UNAUTHORIZED:
raise ErrAtlasUnauthorized(c, details)
elif c == Settings.FORBIDDEN:
raise ErrAtlasForbidden(c, details)
elif c == Settings.NOTFOUND:
raise ErrAtlasNotFound(c, details)
elif c == Settings.METHOD_NOT_ALLOWED:
raise ErrAtlasMethodNotAllowed(c, details)
elif c == Settings.CONFLICT:
raise ErrAtlasConflict(c, details)
else:
# Settings.SERVER_ERRORS
raise ErrAtlasServerErrors(c, details) | python | def answer(self, c, details):
"""Answer will provide all necessary feedback for the caller
Args:
c (int): HTTP Code
details (dict): Response payload
Returns:
dict: Response payload
Raises:
ErrAtlasBadRequest
ErrAtlasUnauthorized
ErrAtlasForbidden
ErrAtlasNotFound
ErrAtlasMethodNotAllowed
ErrAtlasConflict
ErrAtlasServerErrors
"""
if c in [Settings.SUCCESS, Settings.CREATED, Settings.ACCEPTED]:
return details
elif c == Settings.BAD_REQUEST:
raise ErrAtlasBadRequest(c, details)
elif c == Settings.UNAUTHORIZED:
raise ErrAtlasUnauthorized(c, details)
elif c == Settings.FORBIDDEN:
raise ErrAtlasForbidden(c, details)
elif c == Settings.NOTFOUND:
raise ErrAtlasNotFound(c, details)
elif c == Settings.METHOD_NOT_ALLOWED:
raise ErrAtlasMethodNotAllowed(c, details)
elif c == Settings.CONFLICT:
raise ErrAtlasConflict(c, details)
else:
# Settings.SERVER_ERRORS
raise ErrAtlasServerErrors(c, details) | [
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mickybart/python-atlasapi | atlasapi/network.py | Network.get | def get(self, uri):
"""Get request
Args:
uri (str): URI
Returns:
Json: API response
Raises:
Exception: Network issue
"""
r = None
try:
r = requests.get(uri,
allow_redirects=True,
timeout=Settings.requests_timeout,
headers={},
auth=HTTPDigestAuth(self.user, self.password))
return self.answer(r.status_code, r.json())
except:
raise
finally:
if r:
r.connection.close() | python | def get(self, uri):
"""Get request
Args:
uri (str): URI
Returns:
Json: API response
Raises:
Exception: Network issue
"""
r = None
try:
r = requests.get(uri,
allow_redirects=True,
timeout=Settings.requests_timeout,
headers={},
auth=HTTPDigestAuth(self.user, self.password))
return self.answer(r.status_code, r.json())
except:
raise
finally:
if r:
r.connection.close() | [
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kejbaly2/metrique | metrique/cubes/gitdata/commit.py | Commit.get_objects | def get_objects(self, uri, pull=True, **kwargs):
'''
Walk through repo commits to generate a list of repo commit
objects.
Each object has the following properties:
* repo uri
* general commit info
* files added, removed fnames
* lines added, removed
* acked_by
* signed_off_by
* resolves
* related
'''
self.repo = repo = git_clone(uri, pull=pull, reflect=True)
# get a full list of all commit SHAs in the repo (all branches)
cmd = 'git rev-list --all'
output = sys_call(cmd, cwd=repo.path)
repo_shas = set(x.strip() for x in output.split('\n') if x)
logger.debug("Total Commits: %s" % len(repo_shas))
cmd = 'git --no-pager log --all --format=sha:%H --numstat'
output = sys_call(cmd)
all_logs = re.sub('\n+', '\n', output)
c_logs = [x for x in [s.strip() for s in all_logs.split('sha:')] if x]
_end = None # once was true, always is true...
objs = []
for c_log in c_logs:
sha, s, all_changes = c_log.partition('\n')
#try:
c = repo.get_object(sha)
# FIXME: not normalizing to UTC
_start = ts2dt(c.commit_time)
#except Exception as e:
# _start = now
# obj = dict(_oid=sha, _start=_start, _end=_end,
# repo_uri=uri, _e={sha: to_encoding(e)})
# self.objects.add(obj)
# continue
# and some basic stuff...
obj = dict(_oid=sha, _start=_start, _end=_end,
repo_uri=uri, tree=c.tree, parents=c.parents,
author=c.author, committer=c.committer,
author_time=c.author_time, message=c.message,
mergetag=c.mergetag, extra=c.extra)
for _file in all_changes.split('\n'):
_file = _file.strip()
obj.setdefault('files', {})
if not _file:
added, removed, fname = 0, 0, None
else:
added, removed, fname = _file.split('\t')
added = 0 if added == '-' else int(added)
removed = 0 if removed == '-' else int(removed)
# FIXME: sql doesn't nest well..
changes = {'added': added,
'removed': removed}
obj['files'][fname] = changes
# file +/- totals
obj['added'] = sum(
[v.get('added', 0) for v in obj['files'].itervalues()])
obj['removed'] = sum(
[v.get('removed', 0) for v in obj['files'].itervalues()])
# extract interesting bits from the message
obj['acked_by'] = acked_by_re.findall(c.message)
obj['signed_off_by'] = signed_off_by_re.findall(c.message)
obj['resolves'] = resolves_re.findall(c.message)
obj['related'] = related_re.findall(c.message)
objs.append(obj)
self.objects.extend(objs)
return super(Commit, self).get_objects(**kwargs) | python | def get_objects(self, uri, pull=True, **kwargs):
'''
Walk through repo commits to generate a list of repo commit
objects.
Each object has the following properties:
* repo uri
* general commit info
* files added, removed fnames
* lines added, removed
* acked_by
* signed_off_by
* resolves
* related
'''
self.repo = repo = git_clone(uri, pull=pull, reflect=True)
# get a full list of all commit SHAs in the repo (all branches)
cmd = 'git rev-list --all'
output = sys_call(cmd, cwd=repo.path)
repo_shas = set(x.strip() for x in output.split('\n') if x)
logger.debug("Total Commits: %s" % len(repo_shas))
cmd = 'git --no-pager log --all --format=sha:%H --numstat'
output = sys_call(cmd)
all_logs = re.sub('\n+', '\n', output)
c_logs = [x for x in [s.strip() for s in all_logs.split('sha:')] if x]
_end = None # once was true, always is true...
objs = []
for c_log in c_logs:
sha, s, all_changes = c_log.partition('\n')
#try:
c = repo.get_object(sha)
# FIXME: not normalizing to UTC
_start = ts2dt(c.commit_time)
#except Exception as e:
# _start = now
# obj = dict(_oid=sha, _start=_start, _end=_end,
# repo_uri=uri, _e={sha: to_encoding(e)})
# self.objects.add(obj)
# continue
# and some basic stuff...
obj = dict(_oid=sha, _start=_start, _end=_end,
repo_uri=uri, tree=c.tree, parents=c.parents,
author=c.author, committer=c.committer,
author_time=c.author_time, message=c.message,
mergetag=c.mergetag, extra=c.extra)
for _file in all_changes.split('\n'):
_file = _file.strip()
obj.setdefault('files', {})
if not _file:
added, removed, fname = 0, 0, None
else:
added, removed, fname = _file.split('\t')
added = 0 if added == '-' else int(added)
removed = 0 if removed == '-' else int(removed)
# FIXME: sql doesn't nest well..
changes = {'added': added,
'removed': removed}
obj['files'][fname] = changes
# file +/- totals
obj['added'] = sum(
[v.get('added', 0) for v in obj['files'].itervalues()])
obj['removed'] = sum(
[v.get('removed', 0) for v in obj['files'].itervalues()])
# extract interesting bits from the message
obj['acked_by'] = acked_by_re.findall(c.message)
obj['signed_off_by'] = signed_off_by_re.findall(c.message)
obj['resolves'] = resolves_re.findall(c.message)
obj['related'] = related_re.findall(c.message)
objs.append(obj)
self.objects.extend(objs)
return super(Commit, self).get_objects(**kwargs) | [
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zardus/idalink | idalink/memory.py | _dict_values_sorted_by_key | def _dict_values_sorted_by_key(dictionary):
# This should be a yield from instead.
"""Internal helper to return the values of a dictionary, sorted by key.
"""
for _, value in sorted(dictionary.iteritems(), key=operator.itemgetter(0)):
yield value | python | def _dict_values_sorted_by_key(dictionary):
# This should be a yield from instead.
"""Internal helper to return the values of a dictionary, sorted by key.
"""
for _, value in sorted(dictionary.iteritems(), key=operator.itemgetter(0)):
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zardus/idalink | idalink/memory.py | _ondemand | def _ondemand(f):
"""Decorator to only request information if not in cache already.
"""
name = f.__name__
def func(self, *args, **kwargs):
if not args and not kwargs:
if hasattr(self, '_%s' % name):
return getattr(self, '_%s' % name)
a = f(self, *args, **kwargs)
setattr(self, '_%s' % name, a)
return a
else:
return f(self, *args, **kwargs)
func.__name__ = name
return func | python | def _ondemand(f):
"""Decorator to only request information if not in cache already.
"""
name = f.__name__
def func(self, *args, **kwargs):
if not args and not kwargs:
if hasattr(self, '_%s' % name):
return getattr(self, '_%s' % name)
a = f(self, *args, **kwargs)
setattr(self, '_%s' % name, a)
return a
else:
return f(self, *args, **kwargs)
func.__name__ = name
return func | [
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zardus/idalink | idalink/memory.py | CachedIDAMemory.get_memory | def get_memory(self, start, size):
"""Retrieve an area of memory from IDA.
Returns a sparse dictionary of address -> value.
"""
LOG.debug('get_memory: %d bytes from %x', size, start)
return get_memory(self.ida.idaapi, start, size,
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"""Retrieve an area of memory from IDA.
Returns a sparse dictionary of address -> value.
"""
LOG.debug('get_memory: %d bytes from %x', size, start)
return get_memory(self.ida.idaapi, start, size,
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kejbaly2/metrique | metrique/cubes/osinfo/rpm.py | Rpm.get_objects | def get_objects(self, **kwargs):
'''
Run `rpm -q` command on a {local, remote} system to get back
details of installed RPMs.
Default rpm details extracted are as follows:
* name
* version
* release
* arch
* nvra
* license
* os
* packager
* platform
* sourcepackage
* sourcerpm
* summary
'''
fmt = ':::'.join('%%{%s}' % f for f in self._fields)
if self.ssh_host:
output = self._ssh_cmd(fmt)
else:
output = self._local_cmd(fmt)
if isinstance(output, basestring):
output = unicode(output, 'utf-8')
output = output.strip().split('\n')
lines = [l.strip().split(':::') for l in output]
now = utcnow()
host = self.ssh_host or socket.gethostname()
for line in lines:
obj = {'host': host, '_start': now}
for i, item in enumerate(line):
if item == '(none)':
item = None
obj[self._fields[i]] = item
obj['_oid'] = '%s__%s' % (host, obj['nvra'])
self.objects.add(obj)
return super(Rpm, self).get_objects(**kwargs) | python | def get_objects(self, **kwargs):
'''
Run `rpm -q` command on a {local, remote} system to get back
details of installed RPMs.
Default rpm details extracted are as follows:
* name
* version
* release
* arch
* nvra
* license
* os
* packager
* platform
* sourcepackage
* sourcerpm
* summary
'''
fmt = ':::'.join('%%{%s}' % f for f in self._fields)
if self.ssh_host:
output = self._ssh_cmd(fmt)
else:
output = self._local_cmd(fmt)
if isinstance(output, basestring):
output = unicode(output, 'utf-8')
output = output.strip().split('\n')
lines = [l.strip().split(':::') for l in output]
now = utcnow()
host = self.ssh_host or socket.gethostname()
for line in lines:
obj = {'host': host, '_start': now}
for i, item in enumerate(line):
if item == '(none)':
item = None
obj[self._fields[i]] = item
obj['_oid'] = '%s__%s' % (host, obj['nvra'])
self.objects.add(obj)
return super(Rpm, self).get_objects(**kwargs) | [
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EndurantDevs/webargs-sanic | examples/user_simple_storage/extentions/exceptions.py | handle_404 | def handle_404(request, exception):
'''Handle 404 Not Found
This handler should be used to handle error http 404 not found for all
endpoints or if resource not available.
'''
error = format_error(title='Resource not found', detail=str(exception))
return json(return_an_error(error), status=HTTPStatus.NOT_FOUND) | python | def handle_404(request, exception):
'''Handle 404 Not Found
This handler should be used to handle error http 404 not found for all
endpoints or if resource not available.
'''
error = format_error(title='Resource not found', detail=str(exception))
return json(return_an_error(error), status=HTTPStatus.NOT_FOUND) | [
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dailymuse/oz | oz/__init__.py | _add_to_dict | def _add_to_dict(t, container, name, value):
"""
Adds an item to a dictionary, or raises an exception if an item with the
specified key already exists in the dictionary.
"""
if name in container:
raise Exception("%s '%s' already exists" % (t, name))
else:
container[name] = value | python | def _add_to_dict(t, container, name, value):
"""
Adds an item to a dictionary, or raises an exception if an item with the
specified key already exists in the dictionary.
"""
if name in container:
raise Exception("%s '%s' already exists" % (t, name))
else:
container[name] = value | [
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dailymuse/oz | oz/__init__.py | initialize | def initialize(config=None):
"""Initializes oz"""
# Load the config file
if config == None:
config = {}
config_source = None
try:
with open(os.environ.get("OZ_CONFIG", "config.py")) as f:
config_source = f.read()
except Exception:
tornado.log.gen_log.info("Could not read config.py", exc_info=True)
if config_source != None:
tornado.util.exec_in(config_source, config, config)
# Load the plugins
for p in config.get("plugins", ["oz.core"]):
plugin(p)
# Set the options
for key, value in config.get("app_options", {}).items():
setattr(tornado.options.options, key, value)
# Generate the application settings
global settings
settings = tornado.options.options.as_dict()
settings["ui_modules"] = _uimodules
settings["project_name"] = config.get("project_name") | python | def initialize(config=None):
"""Initializes oz"""
# Load the config file
if config == None:
config = {}
config_source = None
try:
with open(os.environ.get("OZ_CONFIG", "config.py")) as f:
config_source = f.read()
except Exception:
tornado.log.gen_log.info("Could not read config.py", exc_info=True)
if config_source != None:
tornado.util.exec_in(config_source, config, config)
# Load the plugins
for p in config.get("plugins", ["oz.core"]):
plugin(p)
# Set the options
for key, value in config.get("app_options", {}).items():
setattr(tornado.options.options, key, value)
# Generate the application settings
global settings
settings = tornado.options.options.as_dict()
settings["ui_modules"] = _uimodules
settings["project_name"] = config.get("project_name") | [
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dailymuse/oz | oz/__init__.py | RequestHandler.trigger | def trigger(self, name, *args, **kwargs):
"""
Triggers an event to run through middleware. This method will execute
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"""
# Relevant middleware is cached so we don't have to rediscover it
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listeners = self._triggers.get(name, [])
# Execute each piece of middleware
for listener in listeners:
result = listener(*args, **kwargs)
if result == break_trigger:
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return True | python | def trigger(self, name, *args, **kwargs):
"""
Triggers an event to run through middleware. This method will execute
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returns the `break_trigger`.
"""
# Relevant middleware is cached so we don't have to rediscover it
# every time. Fetch the cached value if possible.
listeners = self._triggers.get(name, [])
# Execute each piece of middleware
for listener in listeners:
result = listener(*args, **kwargs)
if result == break_trigger:
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return True | [
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michaelpb/omnic | omnic/types/resource.py | Resource.cache_makedirs | def cache_makedirs(self, subdir=None):
'''
Make necessary directories to hold cache value
'''
if subdir is not None:
dirname = self.cache_path
if subdir:
dirname = os.path.join(dirname, subdir)
else:
dirname = os.path.dirname(self.cache_path)
os.makedirs(dirname, exist_ok=True) | python | def cache_makedirs(self, subdir=None):
'''
Make necessary directories to hold cache value
'''
if subdir is not None:
dirname = self.cache_path
if subdir:
dirname = os.path.join(dirname, subdir)
else:
dirname = os.path.dirname(self.cache_path)
os.makedirs(dirname, exist_ok=True) | [
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dailymuse/oz | oz/sqlalchemy/__init__.py | session | def session(connection_string=None):
"""Gets a SQLAlchemy session"""
global _session_makers
connection_string = connection_string or oz.settings["db"]
if not connection_string in _session_makers:
_session_makers[connection_string] = sessionmaker(bind=engine(connection_string=connection_string))
return _session_makers[connection_string]() | python | def session(connection_string=None):
"""Gets a SQLAlchemy session"""
global _session_makers
connection_string = connection_string or oz.settings["db"]
if not connection_string in _session_makers:
_session_makers[connection_string] = sessionmaker(bind=engine(connection_string=connection_string))
return _session_makers[connection_string]() | [
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biocore/burrito-fillings | bfillings/blat.py | assign_reads_to_database | def assign_reads_to_database(query_fasta_fp, database_fasta_fp, output_fp,
params=None):
"""Assign a set of query sequences to a reference database
query_fasta_fp : absolute file path to query sequences
database_fasta_fp : absolute file path to the reference database
output_fp : absolute file path of the output file to write
params : dict of BLAT specific parameters.
This method returns an open file object. The output format
defaults to blast9 and should be parsable by the PyCogent BLAST parsers.
"""
if params is None:
params = {}
if '-out' not in params:
params['-out'] = 'blast9'
blat = Blat(params=params)
result = blat([query_fasta_fp, database_fasta_fp, output_fp])
return result['output'] | python | def assign_reads_to_database(query_fasta_fp, database_fasta_fp, output_fp,
params=None):
"""Assign a set of query sequences to a reference database
query_fasta_fp : absolute file path to query sequences
database_fasta_fp : absolute file path to the reference database
output_fp : absolute file path of the output file to write
params : dict of BLAT specific parameters.
This method returns an open file object. The output format
defaults to blast9 and should be parsable by the PyCogent BLAST parsers.
"""
if params is None:
params = {}
if '-out' not in params:
params['-out'] = 'blast9'
blat = Blat(params=params)
result = blat([query_fasta_fp, database_fasta_fp, output_fp])
return result['output'] | [
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biocore/burrito-fillings | bfillings/blat.py | assign_dna_reads_to_dna_database | def assign_dna_reads_to_dna_database(query_fasta_fp, database_fasta_fp,
output_fp, params=None):
"""Assign DNA reads to a database fasta of DNA sequences.
Wraps assign_reads_to_database, setting database and query types. All
parameters are set to default unless params is passed.
query_fasta_fp: absolute path to the query fasta file containing DNA
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database_fasta_fp: absolute path to the database fasta file containing
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output_fp: absolute path where the output file will be generated.
params: optional. dict containing parameter settings to be used
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This method returns an open file object. The output format
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"""
if params is None:
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}
# if the user specified parameters other than default, then use them.
# However, if they try to change the database or query types, raise an
# applciation error.
if '-t' in params or '-q' in params:
raise ApplicationError("Cannot change database or query types when " +
"using assign_dna_reads_to_dna_database. " +
"Use assign_reads_to_database instead.\n")
my_params.update(params)
result = assign_reads_to_database(query_fasta_fp, database_fasta_fp,
output_fp, my_params)
return result | python | def assign_dna_reads_to_dna_database(query_fasta_fp, database_fasta_fp,
output_fp, params=None):
"""Assign DNA reads to a database fasta of DNA sequences.
Wraps assign_reads_to_database, setting database and query types. All
parameters are set to default unless params is passed.
query_fasta_fp: absolute path to the query fasta file containing DNA
sequences.
database_fasta_fp: absolute path to the database fasta file containing
DNA sequences.
output_fp: absolute path where the output file will be generated.
params: optional. dict containing parameter settings to be used
instead of default values. Cannot change database or query
file types from dna and dna, respectively.
This method returns an open file object. The output format
defaults to blast9 and should be parsable by the PyCogent BLAST parsers.
"""
if params is None:
params = {}
my_params = {'-t': 'dna',
'-q': 'dna'
}
# if the user specified parameters other than default, then use them.
# However, if they try to change the database or query types, raise an
# applciation error.
if '-t' in params or '-q' in params:
raise ApplicationError("Cannot change database or query types when " +
"using assign_dna_reads_to_dna_database. " +
"Use assign_reads_to_database instead.\n")
my_params.update(params)
result = assign_reads_to_database(query_fasta_fp, database_fasta_fp,
output_fp, my_params)
return result | [
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biocore/burrito-fillings | bfillings/blat.py | assign_dna_reads_to_protein_database | def assign_dna_reads_to_protein_database(query_fasta_fp, database_fasta_fp,
output_fp, temp_dir="/tmp", params=None):
"""Assign DNA reads to a database fasta of protein sequences.
Wraps assign_reads_to_database, setting database and query types. All
parameters are set to default unless params is passed. A temporary
file must be written containing the translated sequences from the input
query fasta file because BLAT cannot do this automatically.
query_fasta_fp: absolute path to the query fasta file containing DNA
sequences.
database_fasta_fp: absolute path to the database fasta file containing
protein sequences.
output_fp: absolute path where the output file will be generated.
temp_dir: optional. Change the location where the translated sequences
will be written before being used as the query. Defaults to
/tmp.
params: optional. dict containing parameter settings to be used
instead of default values. Cannot change database or query
file types from protein and dna, respectively.
This method returns an open file object. The output format
defaults to blast9 and should be parsable by the PyCogent BLAST parsers.
"""
if params is None:
params = {}
my_params = {'-t': 'prot', '-q': 'prot'}
# make sure temp_dir specifies an absolute path
if not isabs(temp_dir):
raise ApplicationError("temp_dir must be an absolute path.")
# if the user specified parameters other than default, then use them.
# However, if they try to change the database or query types, raise an
# applciation error.
if '-t' in params or '-q' in params:
raise ApplicationError("Cannot change database or query types "
"when using assign_dna_reads_to_dna_database. Use "
"assign_reads_to_database instead.")
if 'genetic_code' in params:
my_genetic_code = GeneticCodes[params['genetic_code']]
del params['genetic_code']
else:
my_genetic_code = GeneticCodes[1]
my_params.update(params)
# get six-frame translation of the input DNA sequences and write them to
# temporary file.
_, tmp = mkstemp(dir=temp_dir)
tmp_out = open(tmp, 'w')
for label, sequence in parse_fasta(open(query_fasta_fp)):
seq_id = label.split()[0]
s = DNA.makeSequence(sequence)
translations = my_genetic_code.sixframes(s)
frames = [1, 2, 3, -1, -2, -3]
translations = dict(zip(frames, translations))
for frame, translation in sorted(translations.iteritems()):
entry = '>{seq_id}_frame_{frame}\n{trans}\n'
entry = entry.format(seq_id=seq_id, frame=frame, trans=translation)
tmp_out.write(entry)
tmp_out.close()
result = assign_reads_to_database(tmp, database_fasta_fp, output_fp,
params=my_params)
remove(tmp)
return result | python | def assign_dna_reads_to_protein_database(query_fasta_fp, database_fasta_fp,
output_fp, temp_dir="/tmp", params=None):
"""Assign DNA reads to a database fasta of protein sequences.
Wraps assign_reads_to_database, setting database and query types. All
parameters are set to default unless params is passed. A temporary
file must be written containing the translated sequences from the input
query fasta file because BLAT cannot do this automatically.
query_fasta_fp: absolute path to the query fasta file containing DNA
sequences.
database_fasta_fp: absolute path to the database fasta file containing
protein sequences.
output_fp: absolute path where the output file will be generated.
temp_dir: optional. Change the location where the translated sequences
will be written before being used as the query. Defaults to
/tmp.
params: optional. dict containing parameter settings to be used
instead of default values. Cannot change database or query
file types from protein and dna, respectively.
This method returns an open file object. The output format
defaults to blast9 and should be parsable by the PyCogent BLAST parsers.
"""
if params is None:
params = {}
my_params = {'-t': 'prot', '-q': 'prot'}
# make sure temp_dir specifies an absolute path
if not isabs(temp_dir):
raise ApplicationError("temp_dir must be an absolute path.")
# if the user specified parameters other than default, then use them.
# However, if they try to change the database or query types, raise an
# applciation error.
if '-t' in params or '-q' in params:
raise ApplicationError("Cannot change database or query types "
"when using assign_dna_reads_to_dna_database. Use "
"assign_reads_to_database instead.")
if 'genetic_code' in params:
my_genetic_code = GeneticCodes[params['genetic_code']]
del params['genetic_code']
else:
my_genetic_code = GeneticCodes[1]
my_params.update(params)
# get six-frame translation of the input DNA sequences and write them to
# temporary file.
_, tmp = mkstemp(dir=temp_dir)
tmp_out = open(tmp, 'w')
for label, sequence in parse_fasta(open(query_fasta_fp)):
seq_id = label.split()[0]
s = DNA.makeSequence(sequence)
translations = my_genetic_code.sixframes(s)
frames = [1, 2, 3, -1, -2, -3]
translations = dict(zip(frames, translations))
for frame, translation in sorted(translations.iteritems()):
entry = '>{seq_id}_frame_{frame}\n{trans}\n'
entry = entry.format(seq_id=seq_id, frame=frame, trans=translation)
tmp_out.write(entry)
tmp_out.close()
result = assign_reads_to_database(tmp, database_fasta_fp, output_fp,
params=my_params)
remove(tmp)
return result | [
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file must be written containing the translated sequences from the input
query fasta file because BLAT cannot do this automatically.
query_fasta_fp: absolute path to the query fasta file containing DNA
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database_fasta_fp: absolute path to the database fasta file containing
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output_fp: absolute path where the output file will be generated.
temp_dir: optional. Change the location where the translated sequences
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params: optional. dict containing parameter settings to be used
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This method returns an open file object. The output format
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biocore/burrito-fillings | bfillings/blat.py | Blat._get_base_command | def _get_base_command(self):
"""Gets the command that will be run when the app controller is
called.
"""
command_parts = []
cd_command = ''.join(['cd ', str(self.WorkingDir), ';'])
if self._command is None:
raise ApplicationError('_command has not been set.')
command = self._command
parameters = sorted([str(x) for x in self.Parameters.values()
if str(x)])
synonyms = self._synonyms
command_parts.append(cd_command)
command_parts.append(command)
command_parts.append(self._database) # Positional argument
command_parts.append(self._query) # Positional argument
command_parts += parameters
if self._output:
command_parts.append(self._output.Path) # Positional
return (
self._command_delimiter.join(filter(None, command_parts)).strip()
) | python | def _get_base_command(self):
"""Gets the command that will be run when the app controller is
called.
"""
command_parts = []
cd_command = ''.join(['cd ', str(self.WorkingDir), ';'])
if self._command is None:
raise ApplicationError('_command has not been set.')
command = self._command
parameters = sorted([str(x) for x in self.Parameters.values()
if str(x)])
synonyms = self._synonyms
command_parts.append(cd_command)
command_parts.append(command)
command_parts.append(self._database) # Positional argument
command_parts.append(self._query) # Positional argument
command_parts += parameters
if self._output:
command_parts.append(self._output.Path) # Positional
return (
self._command_delimiter.join(filter(None, command_parts)).strip()
) | [
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biocore/burrito-fillings | bfillings/blat.py | Blat._input_as_list | def _input_as_list(self, data):
'''Takes the positional arguments as input in a list.
The list input here should be [query_file_path, database_file_path,
output_file_path]'''
query, database, output = data
if (not isabs(database)) \
or (not isabs(query)) \
or (not isabs(output)):
raise ApplicationError("Only absolute paths allowed.\n%s" %
', '.join(data))
self._database = FilePath(database)
self._query = FilePath(query)
self._output = ResultPath(output, IsWritten=True)
# check parameters that can only take a particular set of values
# check combination of databse and query type
if self.Parameters['-t'].isOn() and self.Parameters['-q'].isOn() and \
(self.Parameters['-t'].Value, self.Parameters['-q'].Value) not in \
self._valid_combinations:
error_message = "Invalid combination of database and query " + \
"types ('%s', '%s').\n" % \
(self.Paramters['-t'].Value,
self.Parameters['-q'].Value)
error_message += "Must be one of: %s\n" % \
repr(self._valid_combinations)
raise ApplicationError(error_message)
# check database type
if self.Parameters['-t'].isOn() and \
self.Parameters['-t'].Value not in self._database_types:
error_message = "Invalid database type %s\n" % \
self.Parameters['-t'].Value
error_message += "Allowed values: %s\n" % \
', '.join(self._database_types)
raise ApplicationError(error_message)
# check query type
if self.Parameters['-q'].isOn() and \
self.Parameters['-q'].Value not in self._query_types:
error_message = "Invalid query type %s\n" % \
self.Parameters['-q'].Value
error_message += "Allowed values: %s\n" % \
', '.join(self._query_types)
raise ApplicationError(error_message)
# check mask type
if self.Parameters['-mask'].isOn() and \
self.Parameters['-mask'].Value not in self._mask_types:
error_message = "Invalid mask type %s\n" % \
self.Parameters['-mask']
error_message += "Allowed Values: %s\n" % \
', '.join(self._mask_types)
raise ApplicationError(error_message)
# check qmask type
if self.Parameters['-qMask'].isOn() and \
self.Parameters['-qMask'].Value not in self._mask_types:
error_message = "Invalid qMask type %s\n" % \
self.Parameters['-qMask'].Value
error_message += "Allowed values: %s\n" % \
', '.join(self._mask_types)
raise ApplicationError(error_message)
# check repeat type
if self.Parameters['-repeats'].isOn() and \
self.Parameters['-repeats'].Value not in self._mask_types:
error_message = "Invalid repeat type %s\n" % \
self.Parameters['-repeat'].Value
error_message += "Allowed values: %s\n" % \
', '.join(self._mask_types)
raise ApplicationError(error_message)
# check output format
if self.Parameters['-out'].isOn() and \
self.Parameters['-out'].Value not in self._out_types:
error_message = "Invalid output type %s\n" % \
self.Parameters['-out']
error_message += "Allowed values: %s\n" % \
', '.join(self._out_types)
raise ApplicationError(error_message)
return '' | python | def _input_as_list(self, data):
'''Takes the positional arguments as input in a list.
The list input here should be [query_file_path, database_file_path,
output_file_path]'''
query, database, output = data
if (not isabs(database)) \
or (not isabs(query)) \
or (not isabs(output)):
raise ApplicationError("Only absolute paths allowed.\n%s" %
', '.join(data))
self._database = FilePath(database)
self._query = FilePath(query)
self._output = ResultPath(output, IsWritten=True)
# check parameters that can only take a particular set of values
# check combination of databse and query type
if self.Parameters['-t'].isOn() and self.Parameters['-q'].isOn() and \
(self.Parameters['-t'].Value, self.Parameters['-q'].Value) not in \
self._valid_combinations:
error_message = "Invalid combination of database and query " + \
"types ('%s', '%s').\n" % \
(self.Paramters['-t'].Value,
self.Parameters['-q'].Value)
error_message += "Must be one of: %s\n" % \
repr(self._valid_combinations)
raise ApplicationError(error_message)
# check database type
if self.Parameters['-t'].isOn() and \
self.Parameters['-t'].Value not in self._database_types:
error_message = "Invalid database type %s\n" % \
self.Parameters['-t'].Value
error_message += "Allowed values: %s\n" % \
', '.join(self._database_types)
raise ApplicationError(error_message)
# check query type
if self.Parameters['-q'].isOn() and \
self.Parameters['-q'].Value not in self._query_types:
error_message = "Invalid query type %s\n" % \
self.Parameters['-q'].Value
error_message += "Allowed values: %s\n" % \
', '.join(self._query_types)
raise ApplicationError(error_message)
# check mask type
if self.Parameters['-mask'].isOn() and \
self.Parameters['-mask'].Value not in self._mask_types:
error_message = "Invalid mask type %s\n" % \
self.Parameters['-mask']
error_message += "Allowed Values: %s\n" % \
', '.join(self._mask_types)
raise ApplicationError(error_message)
# check qmask type
if self.Parameters['-qMask'].isOn() and \
self.Parameters['-qMask'].Value not in self._mask_types:
error_message = "Invalid qMask type %s\n" % \
self.Parameters['-qMask'].Value
error_message += "Allowed values: %s\n" % \
', '.join(self._mask_types)
raise ApplicationError(error_message)
# check repeat type
if self.Parameters['-repeats'].isOn() and \
self.Parameters['-repeats'].Value not in self._mask_types:
error_message = "Invalid repeat type %s\n" % \
self.Parameters['-repeat'].Value
error_message += "Allowed values: %s\n" % \
', '.join(self._mask_types)
raise ApplicationError(error_message)
# check output format
if self.Parameters['-out'].isOn() and \
self.Parameters['-out'].Value not in self._out_types:
error_message = "Invalid output type %s\n" % \
self.Parameters['-out']
error_message += "Allowed values: %s\n" % \
', '.join(self._out_types)
raise ApplicationError(error_message)
return '' | [
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castelao/oceansdb | oceansdb/woa.py | woa_profile_from_dap | def woa_profile_from_dap(var, d, lat, lon, depth, cfg):
"""
Monthly Climatologic Mean and Standard Deviation from WOA,
used either for temperature or salinity.
INPUTS
time: [day of the year]
lat: [-90<lat<90]
lon: [-180<lon<180]
depth: [meters]
Reads the WOA Monthly Climatology NetCDF file and
returns the corresponding WOA values of salinity or temperature mean and
standard deviation for the given time, lat, lon, depth.
"""
if lon < 0:
lon = lon+360
url = cfg['url']
doy = int(d.strftime('%j'))
dataset = open_url(url)
dn = (np.abs(doy-dataset['time'][:])).argmin()
xn = (np.abs(lon-dataset['lon'][:])).argmin()
yn = (np.abs(lat-dataset['lat'][:])).argmin()
if re.match("temperature\d?$", var):
mn = ma.masked_values(dataset.t_mn.t_mn[dn, :, yn, xn].reshape(
dataset['depth'].shape[0]), dataset.t_mn.attributes['_FillValue'])
sd = ma.masked_values(dataset.t_sd.t_sd[dn, :, yn, xn].reshape(
dataset['depth'].shape[0]), dataset.t_sd.attributes['_FillValue'])
# se = ma.masked_values(dataset.t_se.t_se[dn, :, yn, xn].reshape(
# dataset['depth'].shape[0]), dataset.t_se.attributes['_FillValue'])
# Use this in the future. A minimum # of samples
# dd = ma.masked_values(dataset.t_dd.t_dd[dn, :, yn, xn].reshape(
# dataset['depth'].shape[0]), dataset.t_dd.attributes['_FillValue'])
elif re.match("salinity\d?$", var):
mn = ma.masked_values(dataset.s_mn.s_mn[dn, :, yn, xn].reshape(
dataset['depth'].shape[0]), dataset.s_mn.attributes['_FillValue'])
sd = ma.masked_values(dataset.s_sd.s_sd[dn, :, yn, xn].reshape(
dataset['depth'].shape[0]), dataset.s_sd.attributes['_FillValue'])
# dd = ma.masked_values(dataset.s_dd.s_dd[dn, :, yn, xn].reshape(
# dataset['depth'].shape[0]), dataset.s_dd.attributes['_FillValue'])
zwoa = ma.array(dataset.depth[:])
ind = (depth <= zwoa.max()) & (depth >= zwoa.min())
# Mean value profile
f = interp1d(zwoa[~ma.getmaskarray(mn)].compressed(), mn.compressed())
mn_interp = ma.masked_all(depth.shape)
mn_interp[ind] = f(depth[ind])
# The stdev profile
f = interp1d(zwoa[~ma.getmaskarray(sd)].compressed(), sd.compressed())
sd_interp = ma.masked_all(depth.shape)
sd_interp[ind] = f(depth[ind])
output = {'woa_an': mn_interp, 'woa_sd': sd_interp}
return output | python | def woa_profile_from_dap(var, d, lat, lon, depth, cfg):
"""
Monthly Climatologic Mean and Standard Deviation from WOA,
used either for temperature or salinity.
INPUTS
time: [day of the year]
lat: [-90<lat<90]
lon: [-180<lon<180]
depth: [meters]
Reads the WOA Monthly Climatology NetCDF file and
returns the corresponding WOA values of salinity or temperature mean and
standard deviation for the given time, lat, lon, depth.
"""
if lon < 0:
lon = lon+360
url = cfg['url']
doy = int(d.strftime('%j'))
dataset = open_url(url)
dn = (np.abs(doy-dataset['time'][:])).argmin()
xn = (np.abs(lon-dataset['lon'][:])).argmin()
yn = (np.abs(lat-dataset['lat'][:])).argmin()
if re.match("temperature\d?$", var):
mn = ma.masked_values(dataset.t_mn.t_mn[dn, :, yn, xn].reshape(
dataset['depth'].shape[0]), dataset.t_mn.attributes['_FillValue'])
sd = ma.masked_values(dataset.t_sd.t_sd[dn, :, yn, xn].reshape(
dataset['depth'].shape[0]), dataset.t_sd.attributes['_FillValue'])
# se = ma.masked_values(dataset.t_se.t_se[dn, :, yn, xn].reshape(
# dataset['depth'].shape[0]), dataset.t_se.attributes['_FillValue'])
# Use this in the future. A minimum # of samples
# dd = ma.masked_values(dataset.t_dd.t_dd[dn, :, yn, xn].reshape(
# dataset['depth'].shape[0]), dataset.t_dd.attributes['_FillValue'])
elif re.match("salinity\d?$", var):
mn = ma.masked_values(dataset.s_mn.s_mn[dn, :, yn, xn].reshape(
dataset['depth'].shape[0]), dataset.s_mn.attributes['_FillValue'])
sd = ma.masked_values(dataset.s_sd.s_sd[dn, :, yn, xn].reshape(
dataset['depth'].shape[0]), dataset.s_sd.attributes['_FillValue'])
# dd = ma.masked_values(dataset.s_dd.s_dd[dn, :, yn, xn].reshape(
# dataset['depth'].shape[0]), dataset.s_dd.attributes['_FillValue'])
zwoa = ma.array(dataset.depth[:])
ind = (depth <= zwoa.max()) & (depth >= zwoa.min())
# Mean value profile
f = interp1d(zwoa[~ma.getmaskarray(mn)].compressed(), mn.compressed())
mn_interp = ma.masked_all(depth.shape)
mn_interp[ind] = f(depth[ind])
# The stdev profile
f = interp1d(zwoa[~ma.getmaskarray(sd)].compressed(), sd.compressed())
sd_interp = ma.masked_all(depth.shape)
sd_interp[ind] = f(depth[ind])
output = {'woa_an': mn_interp, 'woa_sd': sd_interp}
return output | [
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used either for temperature or salinity.
INPUTS
time: [day of the year]
lat: [-90<lat<90]
lon: [-180<lon<180]
depth: [meters]
Reads the WOA Monthly Climatology NetCDF file and
returns the corresponding WOA values of salinity or temperature mean and
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