id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1 value | code stringlengths 51 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
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6,700 | paylogic/pip-accel | pip_accel/__init__.py | PipAccelerator.initialize_directories | def initialize_directories(self):
"""Automatically create local directories required by pip-accel."""
makedirs(self.config.source_index)
makedirs(self.config.eggs_cache) | python | def initialize_directories(self):
makedirs(self.config.source_index)
makedirs(self.config.eggs_cache) | [
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6,701 | paylogic/pip-accel | pip_accel/__init__.py | PipAccelerator.clean_source_index | def clean_source_index(self):
"""
Cleanup broken symbolic links in the local source distribution index.
The purpose of this method requires some context to understand. Let me
preface this by stating that I realize I'm probably overcomplicating
things, but I like to preserve forward / backward compatibility when
possible and I don't feel like dropping everyone's locally cached
source distribution archives without a good reason to do so. With that
out of the way:
- Versions of pip-accel based on pip 1.4.x maintained a local source
distribution index based on a directory containing symbolic links
pointing directly into pip's download cache. When files were removed
from pip's download cache, broken symbolic links remained in
pip-accel's local source distribution index directory. This resulted
in very confusing error messages. To avoid this
:func:`clean_source_index()` cleaned up broken symbolic links
whenever pip-accel was about to invoke pip.
- More recent versions of pip (6.x) no longer support the same style of
download cache that contains source distribution archives that can be
re-used directly by pip-accel. To cope with the changes in pip 6.x
new versions of pip-accel tell pip to download source distribution
archives directly into the local source distribution index directory
maintained by pip-accel.
- It is very reasonable for users of pip-accel to have multiple
versions of pip-accel installed on their system (imagine a dozen
Python virtual environments that won't all be updated at the same
time; this is the situation I always find myself in :-). These
versions of pip-accel will be sharing the same local source
distribution index directory.
- All of this leads up to the local source distribution index directory
containing a mixture of symbolic links and regular files with no
obvious way to atomically and gracefully upgrade the local source
distribution index directory while avoiding fights between old and
new versions of pip-accel :-).
- I could of course switch to storing the new local source distribution
index in a differently named directory (avoiding potential conflicts
between multiple versions of pip-accel) but then I would have to
introduce a new configuration option, otherwise everyone who has
configured pip-accel to store its source index in a non-default
location could still be bitten by compatibility issues.
For now I've decided to keep using the same directory for the local
source distribution index and to keep cleaning up broken symbolic
links. This enables cooperating between old and new versions of
pip-accel and avoids trashing user's local source distribution indexes.
The main disadvantage is that pip-accel is still required to clean up
broken symbolic links...
"""
cleanup_timer = Timer()
cleanup_counter = 0
for entry in os.listdir(self.config.source_index):
pathname = os.path.join(self.config.source_index, entry)
if os.path.islink(pathname) and not os.path.exists(pathname):
logger.warn("Cleaning up broken symbolic link: %s", pathname)
os.unlink(pathname)
cleanup_counter += 1
logger.debug("Cleaned up %i broken symbolic links from source index in %s.", cleanup_counter, cleanup_timer) | python | def clean_source_index(self):
cleanup_timer = Timer()
cleanup_counter = 0
for entry in os.listdir(self.config.source_index):
pathname = os.path.join(self.config.source_index, entry)
if os.path.islink(pathname) and not os.path.exists(pathname):
logger.warn("Cleaning up broken symbolic link: %s", pathname)
os.unlink(pathname)
cleanup_counter += 1
logger.debug("Cleaned up %i broken symbolic links from source index in %s.", cleanup_counter, cleanup_timer) | [
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source distribution archives without a good reason to do so. With that
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pointing directly into pip's download cache. When files were removed
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pip-accel's local source distribution index directory. This resulted
in very confusing error messages. To avoid this
:func:`clean_source_index()` cleaned up broken symbolic links
whenever pip-accel was about to invoke pip.
- More recent versions of pip (6.x) no longer support the same style of
download cache that contains source distribution archives that can be
re-used directly by pip-accel. To cope with the changes in pip 6.x
new versions of pip-accel tell pip to download source distribution
archives directly into the local source distribution index directory
maintained by pip-accel.
- It is very reasonable for users of pip-accel to have multiple
versions of pip-accel installed on their system (imagine a dozen
Python virtual environments that won't all be updated at the same
time; this is the situation I always find myself in :-). These
versions of pip-accel will be sharing the same local source
distribution index directory.
- All of this leads up to the local source distribution index directory
containing a mixture of symbolic links and regular files with no
obvious way to atomically and gracefully upgrade the local source
distribution index directory while avoiding fights between old and
new versions of pip-accel :-).
- I could of course switch to storing the new local source distribution
index in a differently named directory (avoiding potential conflicts
between multiple versions of pip-accel) but then I would have to
introduce a new configuration option, otherwise everyone who has
configured pip-accel to store its source index in a non-default
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For now I've decided to keep using the same directory for the local
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The main disadvantage is that pip-accel is still required to clean up
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6,702 | paylogic/pip-accel | pip_accel/__init__.py | PipAccelerator.install_from_arguments | def install_from_arguments(self, arguments, **kw):
"""
Download, unpack, build and install the specified requirements.
This function is a simple wrapper for :func:`get_requirements()`,
:func:`install_requirements()` and :func:`cleanup_temporary_directories()`
that implements the default behavior of the pip accelerator. If you're
extending or embedding pip-accel you may want to call the underlying
methods instead.
If the requirement set includes wheels and ``setuptools >= 0.8`` is not
yet installed, it will be added to the requirement set and installed
together with the other requirement(s) in order to enable the usage of
distributions installed from wheels (their metadata is different).
:param arguments: The command line arguments to ``pip install ..`` (a
list of strings).
:param kw: Any keyword arguments are passed on to
:func:`install_requirements()`.
:returns: The result of :func:`install_requirements()`.
"""
try:
requirements = self.get_requirements(arguments, use_wheels=self.arguments_allow_wheels(arguments))
have_wheels = any(req.is_wheel for req in requirements)
if have_wheels and not self.setuptools_supports_wheels():
logger.info("Preparing to upgrade to setuptools >= 0.8 to enable wheel support ..")
requirements.extend(self.get_requirements(['setuptools >= 0.8']))
if requirements:
if '--user' in arguments:
from site import USER_BASE
kw.setdefault('prefix', USER_BASE)
return self.install_requirements(requirements, **kw)
else:
logger.info("Nothing to do! (requirements already installed)")
return 0
finally:
self.cleanup_temporary_directories() | python | def install_from_arguments(self, arguments, **kw):
try:
requirements = self.get_requirements(arguments, use_wheels=self.arguments_allow_wheels(arguments))
have_wheels = any(req.is_wheel for req in requirements)
if have_wheels and not self.setuptools_supports_wheels():
logger.info("Preparing to upgrade to setuptools >= 0.8 to enable wheel support ..")
requirements.extend(self.get_requirements(['setuptools >= 0.8']))
if requirements:
if '--user' in arguments:
from site import USER_BASE
kw.setdefault('prefix', USER_BASE)
return self.install_requirements(requirements, **kw)
else:
logger.info("Nothing to do! (requirements already installed)")
return 0
finally:
self.cleanup_temporary_directories() | [
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6,703 | paylogic/pip-accel | pip_accel/__init__.py | PipAccelerator.get_requirements | def get_requirements(self, arguments, max_retries=None, use_wheels=False):
"""
Use pip to download and unpack the requested source distribution archives.
:param arguments: The command line arguments to ``pip install ...`` (a
list of strings).
:param max_retries: The maximum number of times that pip will be asked
to download distribution archives (this helps to
deal with intermittent failures). If this is
:data:`None` then :attr:`~.Config.max_retries` is
used.
:param use_wheels: Whether pip and pip-accel are allowed to use wheels_
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with callers that use pip-accel as a Python API).
.. warning:: Requirements which are already installed are not included
in the result. If this breaks your use case consider using
pip's ``--ignore-installed`` option.
"""
arguments = self.decorate_arguments(arguments)
# Demote hash sum mismatch log messages from CRITICAL to DEBUG (hiding
# implementation details from users unless they want to see them).
with DownloadLogFilter():
with SetupRequiresPatch(self.config, self.eggs_links):
# Use a new build directory for each run of get_requirements().
self.create_build_directory()
# Check whether -U or --upgrade was given.
if any(match_option(a, '-U', '--upgrade') for a in arguments):
logger.info("Checking index(es) for new version (-U or --upgrade was given) ..")
else:
# If -U or --upgrade wasn't given and all requirements can be
# satisfied using the archives in pip-accel's local source
# index we don't need pip to connect to PyPI looking for new
# versions (that will just slow us down).
try:
return self.unpack_source_dists(arguments, use_wheels=use_wheels)
except DistributionNotFound:
logger.info("We don't have all distribution archives yet!")
# Get the maximum number of retries from the configuration if the
# caller didn't specify a preference.
if max_retries is None:
max_retries = self.config.max_retries
# If not all requirements are available locally we use pip to
# download the missing source distribution archives from PyPI (we
# retry a couple of times in case pip reports recoverable
# errors).
for i in range(max_retries):
try:
return self.download_source_dists(arguments, use_wheels=use_wheels)
except Exception as e:
if i + 1 < max_retries:
# On all but the last iteration we swallow exceptions
# during downloading.
logger.warning("pip raised exception while downloading distributions: %s", e)
else:
# On the last iteration we don't swallow exceptions
# during downloading because the error reported by pip
# is the most sensible error for us to report.
raise
logger.info("Retrying after pip failed (%i/%i) ..", i + 1, max_retries) | python | def get_requirements(self, arguments, max_retries=None, use_wheels=False):
arguments = self.decorate_arguments(arguments)
# Demote hash sum mismatch log messages from CRITICAL to DEBUG (hiding
# implementation details from users unless they want to see them).
with DownloadLogFilter():
with SetupRequiresPatch(self.config, self.eggs_links):
# Use a new build directory for each run of get_requirements().
self.create_build_directory()
# Check whether -U or --upgrade was given.
if any(match_option(a, '-U', '--upgrade') for a in arguments):
logger.info("Checking index(es) for new version (-U or --upgrade was given) ..")
else:
# If -U or --upgrade wasn't given and all requirements can be
# satisfied using the archives in pip-accel's local source
# index we don't need pip to connect to PyPI looking for new
# versions (that will just slow us down).
try:
return self.unpack_source_dists(arguments, use_wheels=use_wheels)
except DistributionNotFound:
logger.info("We don't have all distribution archives yet!")
# Get the maximum number of retries from the configuration if the
# caller didn't specify a preference.
if max_retries is None:
max_retries = self.config.max_retries
# If not all requirements are available locally we use pip to
# download the missing source distribution archives from PyPI (we
# retry a couple of times in case pip reports recoverable
# errors).
for i in range(max_retries):
try:
return self.download_source_dists(arguments, use_wheels=use_wheels)
except Exception as e:
if i + 1 < max_retries:
# On all but the last iteration we swallow exceptions
# during downloading.
logger.warning("pip raised exception while downloading distributions: %s", e)
else:
# On the last iteration we don't swallow exceptions
# during downloading because the error reported by pip
# is the most sensible error for us to report.
raise
logger.info("Retrying after pip failed (%i/%i) ..", i + 1, max_retries) | [
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6,704 | paylogic/pip-accel | pip_accel/__init__.py | PipAccelerator.unpack_source_dists | def unpack_source_dists(self, arguments, use_wheels=False):
"""
Find and unpack local source distributions and discover their metadata.
:param arguments: The command line arguments to ``pip install ...`` (a
list of strings).
:param use_wheels: Whether pip and pip-accel are allowed to use wheels_
(:data:`False` by default for backwards compatibility
with callers that use pip-accel as a Python API).
:returns: A list of :class:`pip_accel.req.Requirement` objects.
:raises: Any exceptions raised by pip, for example
:exc:`pip.exceptions.DistributionNotFound` when not all
requirements can be satisfied.
This function checks whether there are local source distributions
available for all requirements, unpacks the source distribution
archives and finds the names and versions of the requirements. By using
the ``pip install --download`` command we avoid reimplementing the
following pip features:
- Parsing of ``requirements.txt`` (including recursive parsing).
- Resolution of possibly conflicting pinned requirements.
- Unpacking source distributions in multiple formats.
- Finding the name & version of a given source distribution.
"""
unpack_timer = Timer()
logger.info("Unpacking distribution(s) ..")
with PatchedAttribute(pip_install_module, 'PackageFinder', CustomPackageFinder):
requirements = self.get_pip_requirement_set(arguments, use_remote_index=False, use_wheels=use_wheels)
logger.info("Finished unpacking %s in %s.", pluralize(len(requirements), "distribution"), unpack_timer)
return requirements | python | def unpack_source_dists(self, arguments, use_wheels=False):
unpack_timer = Timer()
logger.info("Unpacking distribution(s) ..")
with PatchedAttribute(pip_install_module, 'PackageFinder', CustomPackageFinder):
requirements = self.get_pip_requirement_set(arguments, use_remote_index=False, use_wheels=use_wheels)
logger.info("Finished unpacking %s in %s.", pluralize(len(requirements), "distribution"), unpack_timer)
return requirements | [
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6,705 | paylogic/pip-accel | pip_accel/__init__.py | PipAccelerator.download_source_dists | def download_source_dists(self, arguments, use_wheels=False):
"""
Download missing source distributions.
:param arguments: The command line arguments to ``pip install ...`` (a
list of strings).
:param use_wheels: Whether pip and pip-accel are allowed to use wheels_
(:data:`False` by default for backwards compatibility
with callers that use pip-accel as a Python API).
:raises: Any exceptions raised by pip.
"""
download_timer = Timer()
logger.info("Downloading missing distribution(s) ..")
requirements = self.get_pip_requirement_set(arguments, use_remote_index=True, use_wheels=use_wheels)
logger.info("Finished downloading distribution(s) in %s.", download_timer)
return requirements | python | def download_source_dists(self, arguments, use_wheels=False):
download_timer = Timer()
logger.info("Downloading missing distribution(s) ..")
requirements = self.get_pip_requirement_set(arguments, use_remote_index=True, use_wheels=use_wheels)
logger.info("Finished downloading distribution(s) in %s.", download_timer)
return requirements | [
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6,706 | paylogic/pip-accel | pip_accel/__init__.py | PipAccelerator.transform_pip_requirement_set | def transform_pip_requirement_set(self, requirement_set):
"""
Transform pip's requirement set into one that `pip-accel` can work with.
:param requirement_set: The :class:`pip.req.RequirementSet` object
reported by pip.
:returns: A list of :class:`pip_accel.req.Requirement` objects.
This function converts the :class:`pip.req.RequirementSet` object
reported by pip into a list of :class:`pip_accel.req.Requirement`
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"""
filtered_requirements = []
for requirement in requirement_set.requirements.values():
# The `satisfied_by' property is set by pip when a requirement is
# already satisfied (i.e. a version of the package that satisfies
# the requirement is already installed) and -I, --ignore-installed
# is not used. We filter out these requirements because pip never
# unpacks distributions for these requirements, so pip-accel can't
# do anything useful with such requirements.
if requirement.satisfied_by:
continue
# The `constraint' property marks requirement objects that
# constrain the acceptable version(s) of another requirement but
# don't define a requirement themselves, so we filter them out.
if requirement.constraint:
continue
# All other requirements are reported to callers.
filtered_requirements.append(requirement)
self.reported_requirements.append(requirement)
return sorted([Requirement(self.config, r) for r in filtered_requirements],
key=lambda r: r.name.lower()) | python | def transform_pip_requirement_set(self, requirement_set):
filtered_requirements = []
for requirement in requirement_set.requirements.values():
# The `satisfied_by' property is set by pip when a requirement is
# already satisfied (i.e. a version of the package that satisfies
# the requirement is already installed) and -I, --ignore-installed
# is not used. We filter out these requirements because pip never
# unpacks distributions for these requirements, so pip-accel can't
# do anything useful with such requirements.
if requirement.satisfied_by:
continue
# The `constraint' property marks requirement objects that
# constrain the acceptable version(s) of another requirement but
# don't define a requirement themselves, so we filter them out.
if requirement.constraint:
continue
# All other requirements are reported to callers.
filtered_requirements.append(requirement)
self.reported_requirements.append(requirement)
return sorted([Requirement(self.config, r) for r in filtered_requirements],
key=lambda r: r.name.lower()) | [
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:param requirement_set: The :class:`pip.req.RequirementSet` object
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:returns: A list of :class:`pip_accel.req.Requirement` objects.
This function converts the :class:`pip.req.RequirementSet` object
reported by pip into a list of :class:`pip_accel.req.Requirement`
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6,707 | paylogic/pip-accel | pip_accel/__init__.py | PipAccelerator.clear_build_directory | def clear_build_directory(self):
"""Clear the build directory where pip unpacks the source distribution archives."""
stat = os.stat(self.build_directory)
shutil.rmtree(self.build_directory)
os.makedirs(self.build_directory, stat.st_mode) | python | def clear_build_directory(self):
stat = os.stat(self.build_directory)
shutil.rmtree(self.build_directory)
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6,708 | paylogic/pip-accel | pip_accel/__init__.py | PipAccelerator.cleanup_temporary_directories | def cleanup_temporary_directories(self):
"""Delete the build directories and any temporary directories created by pip."""
while self.build_directories:
shutil.rmtree(self.build_directories.pop())
for requirement in self.reported_requirements:
requirement.remove_temporary_source()
while self.eggs_links:
symbolic_link = self.eggs_links.pop()
if os.path.islink(symbolic_link):
os.unlink(symbolic_link) | python | def cleanup_temporary_directories(self):
while self.build_directories:
shutil.rmtree(self.build_directories.pop())
for requirement in self.reported_requirements:
requirement.remove_temporary_source()
while self.eggs_links:
symbolic_link = self.eggs_links.pop()
if os.path.islink(symbolic_link):
os.unlink(symbolic_link) | [
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6,709 | paylogic/pip-accel | pip_accel/__init__.py | DownloadLogFilter.filter | def filter(self, record):
"""Change the severity of selected log records."""
if isinstance(record.msg, basestring):
message = record.msg.lower()
if all(kw in message for kw in self.KEYWORDS):
record.levelname = 'DEBUG'
record.levelno = logging.DEBUG
return 1 | python | def filter(self, record):
if isinstance(record.msg, basestring):
message = record.msg.lower()
if all(kw in message for kw in self.KEYWORDS):
record.levelname = 'DEBUG'
record.levelno = logging.DEBUG
return 1 | [
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6,710 | paylogic/pip-accel | pip_accel/cli.py | main | def main():
"""The command line interface for the ``pip-accel`` program."""
arguments = sys.argv[1:]
# If no arguments are given, the help text of pip-accel is printed.
if not arguments:
usage()
sys.exit(0)
# If no install subcommand is given we pass the command line straight
# to pip without any changes and exit immediately afterwards.
if 'install' not in arguments:
# This will not return.
os.execvp('pip', ['pip'] + arguments)
else:
arguments = [arg for arg in arguments if arg != 'install']
config = Config()
# Initialize logging output.
coloredlogs.install(
fmt=config.log_format,
level=config.log_verbosity,
)
# Adjust verbosity based on -v, -q, --verbose, --quiet options.
for argument in list(arguments):
if match_option(argument, '-v', '--verbose'):
coloredlogs.increase_verbosity()
elif match_option(argument, '-q', '--quiet'):
coloredlogs.decrease_verbosity()
# Perform the requested action(s).
try:
accelerator = PipAccelerator(config)
accelerator.install_from_arguments(arguments)
except NothingToDoError as e:
# Don't print a traceback for this (it's not very user friendly) and
# exit with status zero to stay compatible with pip. For more details
# please refer to https://github.com/paylogic/pip-accel/issues/47.
logger.warning("%s", e)
sys.exit(0)
except Exception:
logger.exception("Caught unhandled exception!")
sys.exit(1) | python | def main():
arguments = sys.argv[1:]
# If no arguments are given, the help text of pip-accel is printed.
if not arguments:
usage()
sys.exit(0)
# If no install subcommand is given we pass the command line straight
# to pip without any changes and exit immediately afterwards.
if 'install' not in arguments:
# This will not return.
os.execvp('pip', ['pip'] + arguments)
else:
arguments = [arg for arg in arguments if arg != 'install']
config = Config()
# Initialize logging output.
coloredlogs.install(
fmt=config.log_format,
level=config.log_verbosity,
)
# Adjust verbosity based on -v, -q, --verbose, --quiet options.
for argument in list(arguments):
if match_option(argument, '-v', '--verbose'):
coloredlogs.increase_verbosity()
elif match_option(argument, '-q', '--quiet'):
coloredlogs.decrease_verbosity()
# Perform the requested action(s).
try:
accelerator = PipAccelerator(config)
accelerator.install_from_arguments(arguments)
except NothingToDoError as e:
# Don't print a traceback for this (it's not very user friendly) and
# exit with status zero to stay compatible with pip. For more details
# please refer to https://github.com/paylogic/pip-accel/issues/47.
logger.warning("%s", e)
sys.exit(0)
except Exception:
logger.exception("Caught unhandled exception!")
sys.exit(1) | [
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6,711 | paylogic/pip-accel | pip_accel/caches/local.py | LocalCacheBackend.get | def get(self, filename):
"""
Check if a distribution archive exists in the local cache.
:param filename: The filename of the distribution archive (a string).
:returns: The pathname of a distribution archive on the local file
system or :data:`None`.
"""
pathname = os.path.join(self.config.binary_cache, filename)
if os.path.isfile(pathname):
logger.debug("Distribution archive exists in local cache (%s).", pathname)
return pathname
else:
logger.debug("Distribution archive doesn't exist in local cache (%s).", pathname)
return None | python | def get(self, filename):
pathname = os.path.join(self.config.binary_cache, filename)
if os.path.isfile(pathname):
logger.debug("Distribution archive exists in local cache (%s).", pathname)
return pathname
else:
logger.debug("Distribution archive doesn't exist in local cache (%s).", pathname)
return None | [
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6,712 | paylogic/pip-accel | pip_accel/caches/local.py | LocalCacheBackend.put | def put(self, filename, handle):
"""
Store a distribution archive in the local cache.
:param filename: The filename of the distribution archive (a string).
:param handle: A file-like object that provides access to the
distribution archive.
"""
file_in_cache = os.path.join(self.config.binary_cache, filename)
logger.debug("Storing distribution archive in local cache: %s", file_in_cache)
makedirs(os.path.dirname(file_in_cache))
# Stream the contents of the distribution archive to a temporary file
# to avoid race conditions (e.g. partial reads) between multiple
# processes that are using the local cache at the same time.
with AtomicReplace(file_in_cache) as temporary_file:
with open(temporary_file, 'wb') as temporary_file_handle:
shutil.copyfileobj(handle, temporary_file_handle)
logger.debug("Finished caching distribution archive in local cache.") | python | def put(self, filename, handle):
file_in_cache = os.path.join(self.config.binary_cache, filename)
logger.debug("Storing distribution archive in local cache: %s", file_in_cache)
makedirs(os.path.dirname(file_in_cache))
# Stream the contents of the distribution archive to a temporary file
# to avoid race conditions (e.g. partial reads) between multiple
# processes that are using the local cache at the same time.
with AtomicReplace(file_in_cache) as temporary_file:
with open(temporary_file, 'wb') as temporary_file_handle:
shutil.copyfileobj(handle, temporary_file_handle)
logger.debug("Finished caching distribution archive in local cache.") | [
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6,713 | fle/django-multi-email-field | multi_email_field/forms.py | MultiEmailField.to_python | def to_python(self, value):
"Normalize data to a list of strings."
# Return None if no input was given.
if not value:
return []
return [v.strip() for v in value.splitlines() if v != ""] | python | def to_python(self, value):
"Normalize data to a list of strings."
# Return None if no input was given.
if not value:
return []
return [v.strip() for v in value.splitlines() if v != ""] | [
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6,714 | fle/django-multi-email-field | multi_email_field/widgets.py | MultiEmailWidget.prep_value | def prep_value(self, value):
""" Prepare value before effectively render widget """
if value in MULTI_EMAIL_FIELD_EMPTY_VALUES:
return ""
elif isinstance(value, six.string_types):
return value
elif isinstance(value, list):
return "\n".join(value)
raise ValidationError('Invalid format.') | python | def prep_value(self, value):
if value in MULTI_EMAIL_FIELD_EMPTY_VALUES:
return ""
elif isinstance(value, six.string_types):
return value
elif isinstance(value, list):
return "\n".join(value)
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6,715 | ElementAI/greensim | greensim/__init__.py | tagged | def tagged(*tags: Tags) -> Callable:
global GREENSIM_TAG_ATTRIBUTE
"""
Decorator for adding a label to the process.
These labels are applied to any child Processes produced by event
"""
def hook(event: Callable):
def wrapper(*args, **kwargs):
event(*args, **kwargs)
setattr(wrapper, GREENSIM_TAG_ATTRIBUTE, tags)
return wrapper
return hook | python | def tagged(*tags: Tags) -> Callable:
global GREENSIM_TAG_ATTRIBUTE
def hook(event: Callable):
def wrapper(*args, **kwargs):
event(*args, **kwargs)
setattr(wrapper, GREENSIM_TAG_ATTRIBUTE, tags)
return wrapper
return hook | [
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6,716 | ElementAI/greensim | greensim/__init__.py | select | def select(*signals: Signal, **kwargs) -> List[Signal]:
"""
Allows the current process to wait for multiple concurrent signals. Waits until one of the signals turns on, at
which point this signal is returned.
:param timeout:
If this parameter is not ``None``, it is taken as a delay at the end of which the process times out, and
stops waiting on the set of :py:class:`Signal`s. In such a situation, a :py:class:`Timeout` exception is raised
on the process.
"""
class CleanUp(Interrupt):
pass
timeout = kwargs.get("timeout", None)
if not isinstance(timeout, (float, int, type(None))):
raise ValueError("The timeout keyword parameter can be either None or a number.")
def wait_one(signal: Signal, common: Signal) -> None:
try:
signal.wait()
common.turn_on()
except CleanUp:
pass
# We simply sets up multiple sub-processes respectively waiting for one of the signals. Once one of them has fired,
# the others will all run no-op eventually, so no need for any explicit clean-up.
common = Signal(name=local.name + "-selector").turn_off()
if _logger is not None:
_log(INFO, "select", "select", "select", signals=[sig.name for sig in signals])
procs = []
for signal in signals:
procs.append(add(wait_one, signal, common))
try:
common.wait(timeout)
finally:
for proc in procs: # Clean up the support processes.
proc.interrupt(CleanUp())
return [signal for signal in signals if signal.is_on] | python | def select(*signals: Signal, **kwargs) -> List[Signal]:
class CleanUp(Interrupt):
pass
timeout = kwargs.get("timeout", None)
if not isinstance(timeout, (float, int, type(None))):
raise ValueError("The timeout keyword parameter can be either None or a number.")
def wait_one(signal: Signal, common: Signal) -> None:
try:
signal.wait()
common.turn_on()
except CleanUp:
pass
# We simply sets up multiple sub-processes respectively waiting for one of the signals. Once one of them has fired,
# the others will all run no-op eventually, so no need for any explicit clean-up.
common = Signal(name=local.name + "-selector").turn_off()
if _logger is not None:
_log(INFO, "select", "select", "select", signals=[sig.name for sig in signals])
procs = []
for signal in signals:
procs.append(add(wait_one, signal, common))
try:
common.wait(timeout)
finally:
for proc in procs: # Clean up the support processes.
proc.interrupt(CleanUp())
return [signal for signal in signals if signal.is_on] | [
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6,717 | ElementAI/greensim | greensim/__init__.py | Simulator.add_in | def add_in(self, delay: float, fn_process: Callable, *args: Any, **kwargs: Any) -> 'Process':
"""
Adds a process to the simulation, which is made to start after the given delay in simulated time.
See method add() for more details.
"""
process = Process(self, fn_process, self._gr)
if _logger is not None:
self._log(INFO, "add", __now=self.now(), fn=fn_process, args=args, kwargs=kwargs)
self._schedule(delay, process.switch, *args, **kwargs)
return process | python | def add_in(self, delay: float, fn_process: Callable, *args: Any, **kwargs: Any) -> 'Process':
process = Process(self, fn_process, self._gr)
if _logger is not None:
self._log(INFO, "add", __now=self.now(), fn=fn_process, args=args, kwargs=kwargs)
self._schedule(delay, process.switch, *args, **kwargs)
return process | [
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6,718 | ElementAI/greensim | greensim/__init__.py | Simulator.add_at | def add_at(self, moment: float, fn_process: Callable, *args: Any, **kwargs: Any) -> 'Process':
"""
Adds a process to the simulation, which is made to start at the given exact time on the simulated clock. Note
that times in the past when compared to the current moment on the simulated clock are forbidden.
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"""
delay = moment - self.now()
if delay < 0.0:
raise ValueError(
f"The given moment to start the process ({moment:f}) is in the past (now is {self.now():f})."
)
return self.add_in(delay, fn_process, *args, **kwargs) | python | def add_at(self, moment: float, fn_process: Callable, *args: Any, **kwargs: Any) -> 'Process':
delay = moment - self.now()
if delay < 0.0:
raise ValueError(
f"The given moment to start the process ({moment:f}) is in the past (now is {self.now():f})."
)
return self.add_in(delay, fn_process, *args, **kwargs) | [
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6,719 | ElementAI/greensim | greensim/__init__.py | Simulator.step | def step(self) -> None:
"""
Runs a single event of the simulation.
"""
event = heappop(self._events)
self._ts_now = event.timestamp or self._ts_now
event.execute(self) | python | def step(self) -> None:
event = heappop(self._events)
self._ts_now = event.timestamp or self._ts_now
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6,720 | ElementAI/greensim | greensim/__init__.py | Simulator.stop | def stop(self) -> None:
"""
Stops the running simulation once the current event is done executing.
"""
if self.is_running:
if _logger is not None:
self._log(INFO, "stop", __now=self.now())
self._is_running = False | python | def stop(self) -> None:
if self.is_running:
if _logger is not None:
self._log(INFO, "stop", __now=self.now())
self._is_running = False | [
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6,721 | ElementAI/greensim | greensim/__init__.py | Simulator._clear | def _clear(self) -> None:
"""
Resets the internal state of the simulator, and sets the simulated clock back to 0.0. This discards all
outstanding events and tears down hanging process instances.
"""
for _, event, _, _ in self.events():
if hasattr(event, "__self__") and isinstance(event.__self__, Process): # type: ignore
event.__self__.throw() # type: ignore
self._events.clear()
self._ts_now = 0.0 | python | def _clear(self) -> None:
for _, event, _, _ in self.events():
if hasattr(event, "__self__") and isinstance(event.__self__, Process): # type: ignore
event.__self__.throw() # type: ignore
self._events.clear()
self._ts_now = 0.0 | [
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6,722 | ElementAI/greensim | greensim/__init__.py | Process.current | def current() -> 'Process':
"""
Returns the instance of the process that is executing at the current moment.
"""
curr = greenlet.getcurrent()
if not isinstance(curr, Process):
raise TypeError("Current greenlet does not correspond to a Process instance.")
return cast(Process, greenlet.getcurrent()) | python | def current() -> 'Process':
curr = greenlet.getcurrent()
if not isinstance(curr, Process):
raise TypeError("Current greenlet does not correspond to a Process instance.")
return cast(Process, greenlet.getcurrent()) | [
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6,723 | ElementAI/greensim | greensim/__init__.py | Signal.turn_on | def turn_on(self) -> "Signal":
"""
Turns on the signal. If processes are waiting, they are all resumed. This may be invoked from any code.
Remark that while processes are simultaneously resumed in simulated time, they are effectively resumed in the
sequence corresponding to the queue discipline. Therefore, if one of the resumed processes turns the signal back
off, remaining resumed processes join back the queue. If the queue discipline is not monotonic (for instance,
if it bears a random component), then this toggling of the signal may reorder the processes.
"""
if _logger is not None:
self._log(INFO, "turn-on")
self._is_on = True
while not self._queue.is_empty():
self._queue.pop()
return self | python | def turn_on(self) -> "Signal":
if _logger is not None:
self._log(INFO, "turn-on")
self._is_on = True
while not self._queue.is_empty():
self._queue.pop()
return self | [
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6,724 | ElementAI/greensim | greensim/__init__.py | Signal.turn_off | def turn_off(self) -> "Signal":
"""
Turns off the signal. This may be invoked from any code.
"""
if _logger is not None:
self._log(INFO, "turn-off")
self._is_on = False
return self | python | def turn_off(self) -> "Signal":
if _logger is not None:
self._log(INFO, "turn-off")
self._is_on = False
return self | [
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6,725 | ElementAI/greensim | greensim/__init__.py | Signal.wait | def wait(self, timeout: Optional[float] = None) -> None:
"""
Makes the current process wait for the signal. If it is closed, it will join the signal's queue.
:param timeout:
If this parameter is not ``None``, it is taken as a delay at the end of which the process times out, and
stops waiting for the :py:class:`Signal`. In such a situation, a :py:class:`Timeout` exception is raised on
the process.
"""
if _logger is not None:
self._log(INFO, "wait")
while not self.is_on:
self._queue.join(timeout) | python | def wait(self, timeout: Optional[float] = None) -> None:
if _logger is not None:
self._log(INFO, "wait")
while not self.is_on:
self._queue.join(timeout) | [
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6,726 | ElementAI/greensim | greensim/__init__.py | Resource.take | def take(self, num_instances: int = 1, timeout: Optional[float] = None) -> None:
"""
The current process reserves a certain number of instances. If there are not enough instances available, the
process is made to join a queue. When this method returns, the process holds the instances it has requested to
take.
:param num_instances:
Number of resource instances to take.
:param timeout:
If this parameter is not ``None``, it is taken as a delay at the end of which the process times out, and
leaves the queue forcibly. In such a situation, a :py:class:`Timeout` exception is raised on the process.
"""
if num_instances < 1:
raise ValueError(f"Process must request at least 1 instance; here requested {num_instances}.")
if num_instances > self.num_instances_total:
raise ValueError(
f"Process must request at most {self.num_instances_total} instances; here requested {num_instances}."
)
if _logger is not None:
self._log(INFO, "take", num_instances=num_instances, free=self.num_instances_free)
proc = Process.current()
if self._num_instances_free < num_instances:
proc.local.__num_instances_required = num_instances
try:
self._waiting.join(timeout)
finally:
del proc.local.__num_instances_required
self._num_instances_free -= num_instances
if _logger is not None and proc in self._usage:
self._log(WARNING, "take-again", already=self._usage[proc], more=num_instances)
self._usage.setdefault(proc, 0)
self._usage[proc] += num_instances | python | def take(self, num_instances: int = 1, timeout: Optional[float] = None) -> None:
if num_instances < 1:
raise ValueError(f"Process must request at least 1 instance; here requested {num_instances}.")
if num_instances > self.num_instances_total:
raise ValueError(
f"Process must request at most {self.num_instances_total} instances; here requested {num_instances}."
)
if _logger is not None:
self._log(INFO, "take", num_instances=num_instances, free=self.num_instances_free)
proc = Process.current()
if self._num_instances_free < num_instances:
proc.local.__num_instances_required = num_instances
try:
self._waiting.join(timeout)
finally:
del proc.local.__num_instances_required
self._num_instances_free -= num_instances
if _logger is not None and proc in self._usage:
self._log(WARNING, "take-again", already=self._usage[proc], more=num_instances)
self._usage.setdefault(proc, 0)
self._usage[proc] += num_instances | [
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6,727 | ElementAI/greensim | greensim/__init__.py | Resource.release | def release(self, num_instances: int = 1) -> None:
"""
The current process releases instances it has previously taken. It may thus release less than it has taken.
These released instances become free. If the total number of free instances then satisfy the request of the top
process of the waiting queue, it is popped off the queue and resumed.
"""
proc = Process.current()
error_format = "Process %s holds %s instances, but requests to release more (%s)"
if self._usage.get(proc, 0) > 0:
if num_instances > self._usage[proc]:
raise ValueError(
error_format % (proc.local.name, self._usage[proc], num_instances)
)
self._usage[proc] -= num_instances
self._num_instances_free += num_instances
if _logger is not None:
self._log(
INFO,
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num_instances=num_instances,
keeping=self._usage[proc],
free=self.num_instances_free
)
if self._usage[proc] <= 0:
del self._usage[proc]
if not self._waiting.is_empty():
num_instances_next = cast(int, self._waiting.peek().local.__num_instances_required)
if num_instances_next <= self.num_instances_free:
self._waiting.pop()
elif _logger is not None:
self._log(DEBUG, "release-nopop", next_requires=num_instances_next, free=self.num_instances_free)
elif _logger is not None:
self._log(DEBUG, "release-queueempty")
else:
raise RuntimeError(
f"Process {proc.local.name} tries to release {num_instances} instances, but is holding none.)"
) | python | def release(self, num_instances: int = 1) -> None:
proc = Process.current()
error_format = "Process %s holds %s instances, but requests to release more (%s)"
if self._usage.get(proc, 0) > 0:
if num_instances > self._usage[proc]:
raise ValueError(
error_format % (proc.local.name, self._usage[proc], num_instances)
)
self._usage[proc] -= num_instances
self._num_instances_free += num_instances
if _logger is not None:
self._log(
INFO,
"release",
num_instances=num_instances,
keeping=self._usage[proc],
free=self.num_instances_free
)
if self._usage[proc] <= 0:
del self._usage[proc]
if not self._waiting.is_empty():
num_instances_next = cast(int, self._waiting.peek().local.__num_instances_required)
if num_instances_next <= self.num_instances_free:
self._waiting.pop()
elif _logger is not None:
self._log(DEBUG, "release-nopop", next_requires=num_instances_next, free=self.num_instances_free)
elif _logger is not None:
self._log(DEBUG, "release-queueempty")
else:
raise RuntimeError(
f"Process {proc.local.name} tries to release {num_instances} instances, but is holding none.)"
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6,728 | ElementAI/greensim | greensim/progress.py | capture_print | def capture_print(file_dest_maybe: Optional[IO] = None):
"""Progress capture that writes updated metrics to an interactive terminal."""
file_dest: IO = file_dest_maybe or sys.stderr
def _print_progress(progress_min: float, rt_remaining: float, _mc: MeasureComparison) -> None:
nonlocal file_dest
percent_progress = progress_min * 100.0
time_remaining, unit = _display_time(rt_remaining)
print(
f"Progress: {percent_progress:.1f}% -- Time remaining: {time_remaining} {unit} ",
end="\r",
file=file_dest
)
return _print_progress | python | def capture_print(file_dest_maybe: Optional[IO] = None):
file_dest: IO = file_dest_maybe or sys.stderr
def _print_progress(progress_min: float, rt_remaining: float, _mc: MeasureComparison) -> None:
nonlocal file_dest
percent_progress = progress_min * 100.0
time_remaining, unit = _display_time(rt_remaining)
print(
f"Progress: {percent_progress:.1f}% -- Time remaining: {time_remaining} {unit} ",
end="\r",
file=file_dest
)
return _print_progress | [
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6,729 | libnano/primer3-py | primer3/wrappers.py | calcTm | def calcTm(seq, mv_conc=50, dv_conc=0, dntp_conc=0.8, dna_conc=50,
max_nn_length=60, tm_method='santalucia',
salt_corrections_method='santalucia'):
''' Return the tm of `seq` as a float.
'''
tm_meth = _tm_methods.get(tm_method)
if tm_meth is None:
raise ValueError('{} is not a valid tm calculation method'.format(
tm_method))
salt_meth = _salt_corrections_methods.get(salt_corrections_method)
if salt_meth is None:
raise ValueError('{} is not a valid salt correction method'.format(
salt_corrections_method))
# For whatever reason mv_conc and dna_conc have to be ints
args = [pjoin(PRIMER3_HOME, 'oligotm'),
'-mv', str(mv_conc),
'-dv', str(dv_conc),
'-n', str(dntp_conc),
'-d', str(dna_conc),
'-tp', str(tm_meth),
'-sc', str(salt_meth),
seq]
tm = subprocess.check_output(args, stderr=DEV_NULL,
env=os.environ)
return float(tm) | python | def calcTm(seq, mv_conc=50, dv_conc=0, dntp_conc=0.8, dna_conc=50,
max_nn_length=60, tm_method='santalucia',
salt_corrections_method='santalucia'):
''' Return the tm of `seq` as a float.
'''
tm_meth = _tm_methods.get(tm_method)
if tm_meth is None:
raise ValueError('{} is not a valid tm calculation method'.format(
tm_method))
salt_meth = _salt_corrections_methods.get(salt_corrections_method)
if salt_meth is None:
raise ValueError('{} is not a valid salt correction method'.format(
salt_corrections_method))
# For whatever reason mv_conc and dna_conc have to be ints
args = [pjoin(PRIMER3_HOME, 'oligotm'),
'-mv', str(mv_conc),
'-dv', str(dv_conc),
'-n', str(dntp_conc),
'-d', str(dna_conc),
'-tp', str(tm_meth),
'-sc', str(salt_meth),
seq]
tm = subprocess.check_output(args, stderr=DEV_NULL,
env=os.environ)
return float(tm) | [
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6,730 | libnano/primer3-py | primer3/wrappers.py | _parse_ntthal | def _parse_ntthal(ntthal_output):
''' Helper method that uses regex to parse ntthal output. '''
parsed_vals = re.search(_ntthal_re, ntthal_output)
return THERMORESULT(
True, # Structure found
float(parsed_vals.group(1)), # dS
float(parsed_vals.group(2)), # dH
float(parsed_vals.group(3)), # dG
float(parsed_vals.group(4)) # tm
) if parsed_vals else NULLTHERMORESULT | python | def _parse_ntthal(ntthal_output):
''' Helper method that uses regex to parse ntthal output. '''
parsed_vals = re.search(_ntthal_re, ntthal_output)
return THERMORESULT(
True, # Structure found
float(parsed_vals.group(1)), # dS
float(parsed_vals.group(2)), # dH
float(parsed_vals.group(3)), # dG
float(parsed_vals.group(4)) # tm
) if parsed_vals else NULLTHERMORESULT | [
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6,731 | libnano/primer3-py | primer3/wrappers.py | calcThermo | def calcThermo(seq1, seq2, calc_type='ANY', mv_conc=50, dv_conc=0,
dntp_conc=0.8, dna_conc=50, temp_c=37, max_loop=30,
temp_only=False):
""" Main subprocess wrapper for calls to the ntthal executable.
Returns a named tuple with tm, ds, dh, and dg values or None if no
structure / complex could be computed.
"""
args = [pjoin(PRIMER3_HOME, 'ntthal'),
'-a', str(calc_type),
'-mv', str(mv_conc),
'-dv', str(dv_conc),
'-n', str(dntp_conc),
'-d', str(dna_conc),
'-t', str(temp_c),
'-maxloop', str(max_loop),
'-path', THERMO_PATH,
'-s1', seq1,
'-s2', seq2]
if temp_only:
args += ['-r']
out = subprocess.check_output(args, stderr=DEV_NULL,
env=os.environ)
return _parse_ntthal(out) | python | def calcThermo(seq1, seq2, calc_type='ANY', mv_conc=50, dv_conc=0,
dntp_conc=0.8, dna_conc=50, temp_c=37, max_loop=30,
temp_only=False):
args = [pjoin(PRIMER3_HOME, 'ntthal'),
'-a', str(calc_type),
'-mv', str(mv_conc),
'-dv', str(dv_conc),
'-n', str(dntp_conc),
'-d', str(dna_conc),
'-t', str(temp_c),
'-maxloop', str(max_loop),
'-path', THERMO_PATH,
'-s1', seq1,
'-s2', seq2]
if temp_only:
args += ['-r']
out = subprocess.check_output(args, stderr=DEV_NULL,
env=os.environ)
return _parse_ntthal(out) | [
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6,732 | libnano/primer3-py | primer3/wrappers.py | calcHairpin | def calcHairpin(seq, mv_conc=50, dv_conc=0, dntp_conc=0.8, dna_conc=50,
temp_c=37, max_loop=30, temp_only=False):
''' Return a namedtuple of the dS, dH, dG, and Tm of any hairpin struct
present.
'''
return calcThermo(seq, seq, 'HAIRPIN', mv_conc, dv_conc, dntp_conc,
dna_conc, temp_c, max_loop, temp_only) | python | def calcHairpin(seq, mv_conc=50, dv_conc=0, dntp_conc=0.8, dna_conc=50,
temp_c=37, max_loop=30, temp_only=False):
''' Return a namedtuple of the dS, dH, dG, and Tm of any hairpin struct
present.
'''
return calcThermo(seq, seq, 'HAIRPIN', mv_conc, dv_conc, dntp_conc,
dna_conc, temp_c, max_loop, temp_only) | [
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6,733 | libnano/primer3-py | primer3/wrappers.py | calcHeterodimer | def calcHeterodimer(seq1, seq2, mv_conc=50, dv_conc=0, dntp_conc=0.8,
dna_conc=50, temp_c=37, max_loop=30, temp_only=False):
''' Return a tuple of the dS, dH, dG, and Tm of any predicted heterodimer.
'''
return calcThermo(seq1, seq2, 'ANY', mv_conc, dv_conc, dntp_conc,
dna_conc, temp_c, max_loop, temp_only) | python | def calcHeterodimer(seq1, seq2, mv_conc=50, dv_conc=0, dntp_conc=0.8,
dna_conc=50, temp_c=37, max_loop=30, temp_only=False):
''' Return a tuple of the dS, dH, dG, and Tm of any predicted heterodimer.
'''
return calcThermo(seq1, seq2, 'ANY', mv_conc, dv_conc, dntp_conc,
dna_conc, temp_c, max_loop, temp_only) | [
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6,734 | libnano/primer3-py | primer3/wrappers.py | designPrimers | def designPrimers(p3_args, input_log=None, output_log=None, err_log=None):
''' Return the raw primer3_core output for the provided primer3 args.
Returns an ordered dict of the boulderIO-format primer3 output file
'''
sp = subprocess.Popen([pjoin(PRIMER3_HOME, 'primer3_core')],
stdout=subprocess.PIPE, stdin=subprocess.PIPE,
stderr=subprocess.STDOUT)
p3_args.setdefault('PRIMER_THERMODYNAMIC_PARAMETERS_PATH',
pjoin(PRIMER3_HOME, 'primer3_config/'))
in_str = _formatBoulderIO(p3_args)
if input_log:
input_log.write(in_str)
input_log.flush()
out_str, err_str = sp.communicate(input=in_str)
if output_log:
output_log.write(out_str)
output_log.flush()
if err_log and err_str is not None:
err_log.write(err_str)
err_log.flush()
return _parseBoulderIO(out_str) | python | def designPrimers(p3_args, input_log=None, output_log=None, err_log=None):
''' Return the raw primer3_core output for the provided primer3 args.
Returns an ordered dict of the boulderIO-format primer3 output file
'''
sp = subprocess.Popen([pjoin(PRIMER3_HOME, 'primer3_core')],
stdout=subprocess.PIPE, stdin=subprocess.PIPE,
stderr=subprocess.STDOUT)
p3_args.setdefault('PRIMER_THERMODYNAMIC_PARAMETERS_PATH',
pjoin(PRIMER3_HOME, 'primer3_config/'))
in_str = _formatBoulderIO(p3_args)
if input_log:
input_log.write(in_str)
input_log.flush()
out_str, err_str = sp.communicate(input=in_str)
if output_log:
output_log.write(out_str)
output_log.flush()
if err_log and err_str is not None:
err_log.write(err_str)
err_log.flush()
return _parseBoulderIO(out_str) | [
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6,735 | libnano/primer3-py | setup.py | makeExecutable | def makeExecutable(fp):
''' Adds the executable bit to the file at filepath `fp`
'''
mode = ((os.stat(fp).st_mode) | 0o555) & 0o7777
setup_log.info("Adding executable bit to %s (mode is now %o)", fp, mode)
os.chmod(fp, mode) | python | def makeExecutable(fp):
''' Adds the executable bit to the file at filepath `fp`
'''
mode = ((os.stat(fp).st_mode) | 0o555) & 0o7777
setup_log.info("Adding executable bit to %s (mode is now %o)", fp, mode)
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6,736 | libnano/primer3-py | primer3/bindings.py | calcHairpin | def calcHairpin(seq, mv_conc=50.0, dv_conc=0.0, dntp_conc=0.8, dna_conc=50.0,
temp_c=37, max_loop=30):
''' Calculate the hairpin formation thermodynamics of a DNA sequence.
**Note that the maximum length of `seq` is 60 bp.** This is a cap suggested
by the Primer3 team as the longest reasonable sequence length for which
a two-state NN model produces reliable results (see primer3/src/libnano/thal.h:50).
Args:
seq (str): DNA sequence to analyze for hairpin formation
mv_conc (float/int, optional): Monovalent cation conc. (mM)
dv_conc (float/int, optional): Divalent cation conc. (mM)
dntp_conc (float/int, optional): dNTP conc. (mM)
dna_conc (float/int, optional): DNA conc. (nM)
temp_c (int, optional): Simulation temperature for dG (Celsius)
max_loop(int, optional): Maximum size of loops in the structure
Returns:
A `ThermoResult` object with thermodynamic characteristics of the
hairpin formation.
Raises:
``RuntimeError``
'''
_setThermoArgs(**locals())
return _THERMO_ANALYSIS.calcHairpin(seq).checkExc() | python | def calcHairpin(seq, mv_conc=50.0, dv_conc=0.0, dntp_conc=0.8, dna_conc=50.0,
temp_c=37, max_loop=30):
''' Calculate the hairpin formation thermodynamics of a DNA sequence.
**Note that the maximum length of `seq` is 60 bp.** This is a cap suggested
by the Primer3 team as the longest reasonable sequence length for which
a two-state NN model produces reliable results (see primer3/src/libnano/thal.h:50).
Args:
seq (str): DNA sequence to analyze for hairpin formation
mv_conc (float/int, optional): Monovalent cation conc. (mM)
dv_conc (float/int, optional): Divalent cation conc. (mM)
dntp_conc (float/int, optional): dNTP conc. (mM)
dna_conc (float/int, optional): DNA conc. (nM)
temp_c (int, optional): Simulation temperature for dG (Celsius)
max_loop(int, optional): Maximum size of loops in the structure
Returns:
A `ThermoResult` object with thermodynamic characteristics of the
hairpin formation.
Raises:
``RuntimeError``
'''
_setThermoArgs(**locals())
return _THERMO_ANALYSIS.calcHairpin(seq).checkExc() | [
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6,737 | libnano/primer3-py | primer3/bindings.py | calcEndStability | def calcEndStability(seq1, seq2, mv_conc=50, dv_conc=0, dntp_conc=0.8,
dna_conc=50, temp_c=37, max_loop=30):
''' Calculate the 3' end stability of DNA sequence `seq1` against DNA
sequence `seq2`.
**Note that at least one of the two sequences must by <60 bp in length.**
This is a cap imposed by Primer3 as the longest reasonable sequence length
for which a two-state NN model produces reliable results (see
primer3/src/libnano/thal.h:50).
Args:
seq1 (str) : DNA sequence to analyze for 3' end
hybridization against the target
sequence
seq2 (str) : Target DNA sequence to analyze for
seq1 3' end hybridization
mv_conc (float/int, optional) : Monovalent cation conc. (mM)
dv_conc (float/int, optional) : Divalent cation conc. (mM)
dntp_conc (float/int, optional) : dNTP conc. (mM)
dna_conc (float/int, optional) : DNA conc. (nM)
temp_c (int, optional) : Simulation temperature for dG (C)
max_loop(int, optional) : Maximum size of loops in the
structure
Returns:
A `ThermoResult` object with thermodynamic characteristics of the
3' hybridization interaction.
Raises:
``RuntimeError``
'''
_setThermoArgs(**locals())
return _THERMO_ANALYSIS.calcEndStability(seq1, seq2).checkExc() | python | def calcEndStability(seq1, seq2, mv_conc=50, dv_conc=0, dntp_conc=0.8,
dna_conc=50, temp_c=37, max_loop=30):
''' Calculate the 3' end stability of DNA sequence `seq1` against DNA
sequence `seq2`.
**Note that at least one of the two sequences must by <60 bp in length.**
This is a cap imposed by Primer3 as the longest reasonable sequence length
for which a two-state NN model produces reliable results (see
primer3/src/libnano/thal.h:50).
Args:
seq1 (str) : DNA sequence to analyze for 3' end
hybridization against the target
sequence
seq2 (str) : Target DNA sequence to analyze for
seq1 3' end hybridization
mv_conc (float/int, optional) : Monovalent cation conc. (mM)
dv_conc (float/int, optional) : Divalent cation conc. (mM)
dntp_conc (float/int, optional) : dNTP conc. (mM)
dna_conc (float/int, optional) : DNA conc. (nM)
temp_c (int, optional) : Simulation temperature for dG (C)
max_loop(int, optional) : Maximum size of loops in the
structure
Returns:
A `ThermoResult` object with thermodynamic characteristics of the
3' hybridization interaction.
Raises:
``RuntimeError``
'''
_setThermoArgs(**locals())
return _THERMO_ANALYSIS.calcEndStability(seq1, seq2).checkExc() | [
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] | 0901c0ef3ac17afd69329d23db71136c00bcb635 | https://github.com/libnano/primer3-py/blob/0901c0ef3ac17afd69329d23db71136c00bcb635/primer3/bindings.py#L167-L201 |
6,738 | libnano/primer3-py | primer3/bindings.py | designPrimers | def designPrimers(seq_args, global_args=None, misprime_lib=None,
mishyb_lib=None, debug=False):
''' Run the Primer3 design process.
If the global args have been previously set (either by a pervious
`designPrimers` call or by a `setGlobals` call), `designPrimers` may be
called with seqArgs alone (as a means of optimization).
Args:
seq_args (dict) : Primer3 sequence/design args as per
Primer3 docs
global_args (dict, optional) : Primer3 global args as per Primer3 docs
misprime_lib (dict, optional) : `Sequence name: sequence` dictionary
for mispriming checks.
mishyb_lib (dict, optional) : `Sequence name: sequence` dictionary
for mishybridization checks.
Returns:
A dictionary of Primer3 results (should be identical to the expected
BoulderIO output from primer3_main)
'''
if global_args:
primerdesign.setGlobals(global_args, misprime_lib, mishyb_lib)
primerdesign.setSeqArgs(seq_args)
return primerdesign.runDesign(debug) | python | def designPrimers(seq_args, global_args=None, misprime_lib=None,
mishyb_lib=None, debug=False):
''' Run the Primer3 design process.
If the global args have been previously set (either by a pervious
`designPrimers` call or by a `setGlobals` call), `designPrimers` may be
called with seqArgs alone (as a means of optimization).
Args:
seq_args (dict) : Primer3 sequence/design args as per
Primer3 docs
global_args (dict, optional) : Primer3 global args as per Primer3 docs
misprime_lib (dict, optional) : `Sequence name: sequence` dictionary
for mispriming checks.
mishyb_lib (dict, optional) : `Sequence name: sequence` dictionary
for mishybridization checks.
Returns:
A dictionary of Primer3 results (should be identical to the expected
BoulderIO output from primer3_main)
'''
if global_args:
primerdesign.setGlobals(global_args, misprime_lib, mishyb_lib)
primerdesign.setSeqArgs(seq_args)
return primerdesign.runDesign(debug) | [
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If the global args have been previously set (either by a pervious
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called with seqArgs alone (as a means of optimization).
Args:
seq_args (dict) : Primer3 sequence/design args as per
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global_args (dict, optional) : Primer3 global args as per Primer3 docs
misprime_lib (dict, optional) : `Sequence name: sequence` dictionary
for mispriming checks.
mishyb_lib (dict, optional) : `Sequence name: sequence` dictionary
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A dictionary of Primer3 results (should be identical to the expected
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6,739 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.unravel_sections | def unravel_sections(section_data):
"""Unravels section type dictionary into flat list of sections with
section type set as an attribute.
Args:
section_data(dict): Data return from py:method::get_sections
Returns:
list: Flat list of sections with ``sectionType`` set to
type (i.e. recitation, lecture, etc)
"""
sections = []
for type, subsection_list in section_data.items():
for section in subsection_list:
section['sectionType'] = type
sections.append(section)
return sections | python | def unravel_sections(section_data):
sections = []
for type, subsection_list in section_data.items():
for section in subsection_list:
section['sectionType'] = type
sections.append(section)
return sections | [
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6,740 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.unravel_staff | def unravel_staff(staff_data):
"""Unravels staff role dictionary into flat list of staff
members with ``role`` set as an attribute.
Args:
staff_data(dict): Data return from py:method::get_staff
Returns:
list: Flat list of staff members with ``role`` set to
role type (i.e. course_admin, instructor, TA, etc)
"""
staff_list = []
for role, staff_members in staff_data['data'].items():
for member in staff_members:
member['role'] = role
staff_list.append(member)
return staff_list | python | def unravel_staff(staff_data):
staff_list = []
for role, staff_members in staff_data['data'].items():
for member in staff_members:
member['role'] = role
staff_list.append(member)
return staff_list | [
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6,741 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.get_gradebook_id | def get_gradebook_id(self, gbuuid):
"""Return gradebookid for a given gradebook uuid.
Args:
gbuuid (str): gradebook uuid, i.e. ``STELLAR:/project/gbngtest``
Raises:
PyLmodUnexpectedData: No gradebook id returned
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
str: value of gradebook id
"""
gradebook = self.get('gradebook', params={'uuid': gbuuid})
if 'data' not in gradebook:
failure_messsage = ('Error in get_gradebook_id '
'for {0} - no data'.format(
gradebook
))
log.error(failure_messsage)
raise PyLmodUnexpectedData(failure_messsage)
return gradebook['data']['gradebookId'] | python | def get_gradebook_id(self, gbuuid):
gradebook = self.get('gradebook', params={'uuid': gbuuid})
if 'data' not in gradebook:
failure_messsage = ('Error in get_gradebook_id '
'for {0} - no data'.format(
gradebook
))
log.error(failure_messsage)
raise PyLmodUnexpectedData(failure_messsage)
return gradebook['data']['gradebookId'] | [
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Raises:
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6,742 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.get_options | def get_options(self, gradebook_id):
"""Get options for gradebook.
Get options dictionary for a gradebook. Options include gradebook
attributes.
Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
Returns:
An example return value is:
.. code-block:: python
{
u'data':
{
u'accessLevel': u'class',
u'archived': False,
u'calc_on_approved_only': False,
u'configured': None,
u'courseName': u'',
u'courseNumber': u'mitxdemosite',
u'deriveOverallGrades': False,
u'gradebookEwsEnabled': False,
u'gradebookId': 1293808,
u'gradebookName': u'Gradebook for mitxdemosite',
u'gradebookReadOnly': False,
u'gradebookVisibleToAdvisors': False,
u'graders_change_approved': False,
u'hideExcuseButtonInUI': False,
u'homeworkBetaEnabled': False,
u'membershipQualifier': u'/project/mitxdemosite',
u'membershipSource': u'stellar',
u'student_sees_actual_grades': True,
u'student_sees_category_info': True,
u'student_sees_comments': True,
u'student_sees_cumulative_score': True,
u'student_sees_histograms': True,
u'student_sees_submissions': False,
u'ta_approves': False,
u'ta_change_approved': False,
u'ta_configures': False,
u'ta_edits': False,
u'use_grade_weighting': False,
u'usingAttendance': False,
u'versionCompatible': 4,
u'versionCompatibleString': u'General Availability'
},
}
"""
end_point = 'gradebook/options/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id)
options = self.get(end_point)
return options['data'] | python | def get_options(self, gradebook_id):
end_point = 'gradebook/options/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id)
options = self.get(end_point)
return options['data'] | [
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Get options dictionary for a gradebook. Options include gradebook
attributes.
Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
Returns:
An example return value is:
.. code-block:: python
{
u'data':
{
u'accessLevel': u'class',
u'archived': False,
u'calc_on_approved_only': False,
u'configured': None,
u'courseName': u'',
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u'gradebookEwsEnabled': False,
u'gradebookId': 1293808,
u'gradebookName': u'Gradebook for mitxdemosite',
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u'graders_change_approved': False,
u'hideExcuseButtonInUI': False,
u'homeworkBetaEnabled': False,
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] | b798b86c33d1eb615e7cd4f3457b5c15da1d86e0 | https://github.com/mitodl/PyLmod/blob/b798b86c33d1eb615e7cd4f3457b5c15da1d86e0/pylmod/gradebook.py#L125-L181 |
6,743 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.get_assignments | def get_assignments(
self,
gradebook_id='',
simple=False,
max_points=True,
avg_stats=False,
grading_stats=False
):
"""Get assignments for a gradebook.
Return list of assignments for a given gradebook,
specified by a py:attribute::gradebook_id. You can control
if additional parameters are returned, but the response
time with py:attribute::avg_stats and py:attribute::grading_stats
enabled is significantly longer.
Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
simple (bool): return just assignment names, default= ``False``
max_points (bool):
Max points is a property of the grading scheme for the
assignment rather than a property of the assignment itself,
default= ``True``
avg_stats (bool): return average grade, default= ``False``
grading_stats (bool):
return grading statistics, i.e. number of approved grades,
unapproved grades, etc., default= ``False``
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: list of assignment dictionaries
An example return value is:
.. code-block:: python
[
{
u'assignmentId': 2431240,
u'categoryId': 1293820,
u'description': u'',
u'dueDate': 1372392000000,
u'dueDateString': u'06-28-2013',
u'gradebookId': 1293808,
u'graderVisible': True,
u'gradingSchemeId': 2431243,
u'gradingSchemeType': u'NUMERIC',
u'isComposite': False,
u'isHomework': False,
u'maxPointsTotal': 10.0,
u'name': u'Homework 1',
u'shortName': u'HW1',
u'userDeleted': False,
u'weight': 1.0
},
{
u'assignmentId': 16708850,
u'categoryId': 1293820,
u'description': u'',
u'dueDate': 1383541200000,
u'dueDateString': u'11-04-2013',
u'gradebookId': 1293808,
u'graderVisible': False,
u'gradingSchemeId': 16708851,
u'gradingSchemeType': u'NUMERIC',
u'isComposite': False,
u'isHomework': False,
u'maxPointsTotal': 100.0,
u'name': u'midterm1',
u'shortName': u'mid1',
u'userDeleted': False,
u'weight': 1.0
},
]
"""
# These are parameters required for the remote API call, so
# there aren't too many arguments
# pylint: disable=too-many-arguments
params = dict(
includeMaxPoints=json.dumps(max_points),
includeAvgStats=json.dumps(avg_stats),
includeGradingStats=json.dumps(grading_stats)
)
assignments = self.get(
'assignments/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
params=params,
)
if simple:
return [{'AssignmentName': x['name']}
for x in assignments['data']]
return assignments['data'] | python | def get_assignments(
self,
gradebook_id='',
simple=False,
max_points=True,
avg_stats=False,
grading_stats=False
):
# These are parameters required for the remote API call, so
# there aren't too many arguments
# pylint: disable=too-many-arguments
params = dict(
includeMaxPoints=json.dumps(max_points),
includeAvgStats=json.dumps(avg_stats),
includeGradingStats=json.dumps(grading_stats)
)
assignments = self.get(
'assignments/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
params=params,
)
if simple:
return [{'AssignmentName': x['name']}
for x in assignments['data']]
return assignments['data'] | [
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Return list of assignments for a given gradebook,
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time with py:attribute::avg_stats and py:attribute::grading_stats
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Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
simple (bool): return just assignment names, default= ``False``
max_points (bool):
Max points is a property of the grading scheme for the
assignment rather than a property of the assignment itself,
default= ``True``
avg_stats (bool): return average grade, default= ``False``
grading_stats (bool):
return grading statistics, i.e. number of approved grades,
unapproved grades, etc., default= ``False``
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: list of assignment dictionaries
An example return value is:
.. code-block:: python
[
{
u'assignmentId': 2431240,
u'categoryId': 1293820,
u'description': u'',
u'dueDate': 1372392000000,
u'dueDateString': u'06-28-2013',
u'gradebookId': 1293808,
u'graderVisible': True,
u'gradingSchemeId': 2431243,
u'gradingSchemeType': u'NUMERIC',
u'isComposite': False,
u'isHomework': False,
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u'weight': 1.0
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{
u'assignmentId': 16708850,
u'categoryId': 1293820,
u'description': u'',
u'dueDate': 1383541200000,
u'dueDateString': u'11-04-2013',
u'gradebookId': 1293808,
u'graderVisible': False,
u'gradingSchemeId': 16708851,
u'gradingSchemeType': u'NUMERIC',
u'isComposite': False,
u'isHomework': False,
u'maxPointsTotal': 100.0,
u'name': u'midterm1',
u'shortName': u'mid1',
u'userDeleted': False,
u'weight': 1.0
},
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6,744 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.get_assignment_by_name | def get_assignment_by_name(self, assignment_name, assignments=None):
"""Get assignment by name.
Get an assignment by name. It works by retrieving all assignments
and returning the first assignment with a matching name. If the
optional parameter ``assignments`` is provided, it uses this
collection rather than retrieving all assignments from the service.
Args:
assignment_name (str): name of assignment
assignments (list): assignments to search, default: None
When ``assignments`` is unspecified, all assignments
are retrieved from the service.
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
tuple: tuple of assignment id and assignment dictionary
.. code-block:: python
(
16708850,
{
u'assignmentId': 16708850,
u'categoryId': 1293820,
u'description': u'',
u'dueDate': 1383541200000,
u'dueDateString': u'11-04-2013',
u'gradebookId': 1293808,
u'graderVisible': False,
u'gradingSchemeId': 16708851,
u'gradingSchemeType': u'NUMERIC',
u'isComposite': False,
u'isHomework': False,
u'maxPointsTotal': 100.0,
u'name': u'midterm1',
u'shortName': u'mid1',
u'userDeleted': False,
u'weight': 1.0
}
)
"""
if assignments is None:
assignments = self.get_assignments()
for assignment in assignments:
if assignment['name'] == assignment_name:
return assignment['assignmentId'], assignment
return None, None | python | def get_assignment_by_name(self, assignment_name, assignments=None):
if assignments is None:
assignments = self.get_assignments()
for assignment in assignments:
if assignment['name'] == assignment_name:
return assignment['assignmentId'], assignment
return None, None | [
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collection rather than retrieving all assignments from the service.
Args:
assignment_name (str): name of assignment
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Raises:
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ValueError: Unable to decode response content
Returns:
tuple: tuple of assignment id and assignment dictionary
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(
16708850,
{
u'assignmentId': 16708850,
u'categoryId': 1293820,
u'description': u'',
u'dueDate': 1383541200000,
u'dueDateString': u'11-04-2013',
u'gradebookId': 1293808,
u'graderVisible': False,
u'gradingSchemeId': 16708851,
u'gradingSchemeType': u'NUMERIC',
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6,745 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.create_assignment | def create_assignment( # pylint: disable=too-many-arguments
self,
name,
short_name,
weight,
max_points,
due_date_str,
gradebook_id='',
**kwargs
):
"""Create a new assignment.
Create a new assignment. By default, assignments are created
under the `Uncategorized` category.
Args:
name (str): descriptive assignment name,
i.e. ``new NUMERIC SIMPLE ASSIGNMENT``
short_name (str): short name of assignment, one word of
no more than 5 characters, i.e. ``SAnew``
weight (str): floating point value for weight, i.e. ``1.0``
max_points (str): floating point value for maximum point
total, i.e. ``100.0``
due_date_str (str): due date as string in ``mm-dd-yyyy``
format, i.e. ``08-21-2011``
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
kwargs (dict): dictionary containing additional parameters,
i.e. ``graderVisible``, ``totalAverage``, and ``categoryId``.
For example:
.. code-block:: python
{
u'graderVisible': True,
u'totalAverage': None
u'categoryId': 1007964,
}
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
dict: dictionary containing ``data``, ``status`` and ``message``
for example:
.. code-block:: python
{
u'data':
{
u'assignmentId': 18490492,
u'categoryId': 1293820,
u'description': u'',
u'dueDate': 1312171200000,
u'dueDateString': u'08-01-2011',
u'gradebookId': 1293808,
u'graderVisible': False,
u'gradingSchemeId': 18490493,
u'gradingSchemeType': u'NUMERIC',
u'isComposite': False,
u'isHomework': False,
u'maxPointsTotal': 100.0,
u'name': u'new NUMERIC SIMPLE ASSIGNMENT',
u'numStudentGradesToBeApproved': 0,
u'numStudentsToBeGraded': 614,
u'shortName': u'SAnew',
u'userDeleted': False,
u'weight': 1.0
},
u'message': u'assignment is created successfully',
u'status': 1
}
"""
data = {
'name': name,
'shortName': short_name,
'weight': weight,
'graderVisible': False,
'gradingSchemeType': 'NUMERIC',
'gradebookId': gradebook_id or self.gradebook_id,
'maxPointsTotal': max_points,
'dueDateString': due_date_str
}
data.update(kwargs)
log.info("Creating assignment %s", name)
response = self.post('assignment', data)
log.debug('Received response data: %s', response)
return response | python | def create_assignment( # pylint: disable=too-many-arguments
self,
name,
short_name,
weight,
max_points,
due_date_str,
gradebook_id='',
**kwargs
):
data = {
'name': name,
'shortName': short_name,
'weight': weight,
'graderVisible': False,
'gradingSchemeType': 'NUMERIC',
'gradebookId': gradebook_id or self.gradebook_id,
'maxPointsTotal': max_points,
'dueDateString': due_date_str
}
data.update(kwargs)
log.info("Creating assignment %s", name)
response = self.post('assignment', data)
log.debug('Received response data: %s', response)
return response | [
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Create a new assignment. By default, assignments are created
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Args:
name (str): descriptive assignment name,
i.e. ``new NUMERIC SIMPLE ASSIGNMENT``
short_name (str): short name of assignment, one word of
no more than 5 characters, i.e. ``SAnew``
weight (str): floating point value for weight, i.e. ``1.0``
max_points (str): floating point value for maximum point
total, i.e. ``100.0``
due_date_str (str): due date as string in ``mm-dd-yyyy``
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gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
kwargs (dict): dictionary containing additional parameters,
i.e. ``graderVisible``, ``totalAverage``, and ``categoryId``.
For example:
.. code-block:: python
{
u'graderVisible': True,
u'totalAverage': None
u'categoryId': 1007964,
}
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
dict: dictionary containing ``data``, ``status`` and ``message``
for example:
.. code-block:: python
{
u'data':
{
u'assignmentId': 18490492,
u'categoryId': 1293820,
u'description': u'',
u'dueDate': 1312171200000,
u'dueDateString': u'08-01-2011',
u'gradebookId': 1293808,
u'graderVisible': False,
u'gradingSchemeId': 18490493,
u'gradingSchemeType': u'NUMERIC',
u'isComposite': False,
u'isHomework': False,
u'maxPointsTotal': 100.0,
u'name': u'new NUMERIC SIMPLE ASSIGNMENT',
u'numStudentGradesToBeApproved': 0,
u'numStudentsToBeGraded': 614,
u'shortName': u'SAnew',
u'userDeleted': False,
u'weight': 1.0
},
u'message': u'assignment is created successfully',
u'status': 1
} | [
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6,746 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.set_grade | def set_grade(
self,
assignment_id,
student_id,
grade_value,
gradebook_id='',
**kwargs
):
"""Set numerical grade for student and assignment.
Set a numerical grade for for a student and assignment. Additional
options
for grade ``mode`` are: OVERALL_GRADE = ``1``, REGULAR_GRADE = ``2``
To set 'excused' as the grade, enter ``None`` for letter and
numeric grade values,
and pass ``x`` as the ``specialGradeValue``.
``ReturnAffectedValues`` flag determines whether or not to return
student cumulative points and
impacted assignment category grades (average and student grade).
Args:
assignment_id (str): numerical ID for assignment
student_id (str): numerical ID for student
grade_value (str): numerical grade value
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
kwargs (dict): dictionary of additional parameters
.. code-block:: python
{
u'letterGradeValue':None,
u'booleanGradeValue':None,
u'specialGradeValue':None,
u'mode':2,
u'isGradeApproved':False,
u'comment':None,
u'returnAffectedValues': True,
}
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
dict: dictionary containing response ``status`` and ``message``
.. code-block:: python
{
u'message': u'grade saved successfully',
u'status': 1
}
"""
# pylint: disable=too-many-arguments
# numericGradeValue stringified because 'x' is a possible
# value for excused grades.
grade_info = {
'studentId': student_id,
'assignmentId': assignment_id,
'mode': 2,
'comment': 'from MITx {0}'.format(time.ctime(time.time())),
'numericGradeValue': str(grade_value),
'isGradeApproved': False
}
grade_info.update(kwargs)
log.info(
"student %s set_grade=%s for assignment %s",
student_id,
grade_value,
assignment_id)
return self.post(
'grades/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
data=grade_info,
) | python | def set_grade(
self,
assignment_id,
student_id,
grade_value,
gradebook_id='',
**kwargs
):
# pylint: disable=too-many-arguments
# numericGradeValue stringified because 'x' is a possible
# value for excused grades.
grade_info = {
'studentId': student_id,
'assignmentId': assignment_id,
'mode': 2,
'comment': 'from MITx {0}'.format(time.ctime(time.time())),
'numericGradeValue': str(grade_value),
'isGradeApproved': False
}
grade_info.update(kwargs)
log.info(
"student %s set_grade=%s for assignment %s",
student_id,
grade_value,
assignment_id)
return self.post(
'grades/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
data=grade_info,
) | [
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Set a numerical grade for for a student and assignment. Additional
options
for grade ``mode`` are: OVERALL_GRADE = ``1``, REGULAR_GRADE = ``2``
To set 'excused' as the grade, enter ``None`` for letter and
numeric grade values,
and pass ``x`` as the ``specialGradeValue``.
``ReturnAffectedValues`` flag determines whether or not to return
student cumulative points and
impacted assignment category grades (average and student grade).
Args:
assignment_id (str): numerical ID for assignment
student_id (str): numerical ID for student
grade_value (str): numerical grade value
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
kwargs (dict): dictionary of additional parameters
.. code-block:: python
{
u'letterGradeValue':None,
u'booleanGradeValue':None,
u'specialGradeValue':None,
u'mode':2,
u'isGradeApproved':False,
u'comment':None,
u'returnAffectedValues': True,
}
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
dict: dictionary containing response ``status`` and ``message``
.. code-block:: python
{
u'message': u'grade saved successfully',
u'status': 1
} | [
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] | b798b86c33d1eb615e7cd4f3457b5c15da1d86e0 | https://github.com/mitodl/PyLmod/blob/b798b86c33d1eb615e7cd4f3457b5c15da1d86e0/pylmod/gradebook.py#L454-L531 |
6,747 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.multi_grade | def multi_grade(self, grade_array, gradebook_id=''):
"""Set multiple grades for students.
Set multiple student grades for a gradebook. The grades are passed
as a list of dictionaries.
Each grade dictionary in ``grade_array`` must contain a
``studentId`` and a ``assignmentId``.
Options for grade mode are: OVERALL_GRADE = ``1``,
REGULAR_GRADE = ``2``
To set 'excused' as the grade, enter ``None`` for
``letterGradeValue`` and ``numericGradeValue``,
and pass ``x`` as the ``specialGradeValue``.
The ``ReturnAffectedValues`` flag determines whether to return
student cumulative points and impacted assignment category
grades (average and student grade)
.. code-block:: python
[
{
u'comment': None,
u'booleanGradeValue': None,
u'studentId': 1135,
u'assignmentId': 4522,
u'specialGradeValue': None,
u'returnAffectedValues': True,
u'letterGradeValue': None,
u'mode': 2,
u'numericGradeValue': 50,
u'isGradeApproved': False
},
{
u'comment': None,
u'booleanGradeValue': None,
u'studentId': 1135,
u'assignmentId': 4522,
u'specialGradeValue': u'x',
u'returnAffectedValues': True,
u'letterGradeValue': None,
u'mode': 2,
u'numericGradeValue': None,
u'isGradeApproved': False
},
{
u'comment': None,
u'booleanGradeValue': None,
u'studentId': 1135,
u'assignmentId': None,
u'specialGradeValue': None,
u'returnAffectedValues': True,
u'letterGradeValue': u'A',
u'mode': 1,
u'numericGradeValue': None,
u'isGradeApproved': False
}
]
Args:
grade_array (dict): an array of grades to save
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
dict: dictionary containing response ``status`` and ``message``
"""
log.info('Sending grades: %r', grade_array)
return self.post(
'multiGrades/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
data=grade_array,
) | python | def multi_grade(self, grade_array, gradebook_id=''):
log.info('Sending grades: %r', grade_array)
return self.post(
'multiGrades/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
data=grade_array,
) | [
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Set multiple student grades for a gradebook. The grades are passed
as a list of dictionaries.
Each grade dictionary in ``grade_array`` must contain a
``studentId`` and a ``assignmentId``.
Options for grade mode are: OVERALL_GRADE = ``1``,
REGULAR_GRADE = ``2``
To set 'excused' as the grade, enter ``None`` for
``letterGradeValue`` and ``numericGradeValue``,
and pass ``x`` as the ``specialGradeValue``.
The ``ReturnAffectedValues`` flag determines whether to return
student cumulative points and impacted assignment category
grades (average and student grade)
.. code-block:: python
[
{
u'comment': None,
u'booleanGradeValue': None,
u'studentId': 1135,
u'assignmentId': 4522,
u'specialGradeValue': None,
u'returnAffectedValues': True,
u'letterGradeValue': None,
u'mode': 2,
u'numericGradeValue': 50,
u'isGradeApproved': False
},
{
u'comment': None,
u'booleanGradeValue': None,
u'studentId': 1135,
u'assignmentId': 4522,
u'specialGradeValue': u'x',
u'returnAffectedValues': True,
u'letterGradeValue': None,
u'mode': 2,
u'numericGradeValue': None,
u'isGradeApproved': False
},
{
u'comment': None,
u'booleanGradeValue': None,
u'studentId': 1135,
u'assignmentId': None,
u'specialGradeValue': None,
u'returnAffectedValues': True,
u'letterGradeValue': u'A',
u'mode': 1,
u'numericGradeValue': None,
u'isGradeApproved': False
}
]
Args:
grade_array (dict): an array of grades to save
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
dict: dictionary containing response ``status`` and ``message`` | [
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] | b798b86c33d1eb615e7cd4f3457b5c15da1d86e0 | https://github.com/mitodl/PyLmod/blob/b798b86c33d1eb615e7cd4f3457b5c15da1d86e0/pylmod/gradebook.py#L533-L609 |
6,748 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.get_sections | def get_sections(self, gradebook_id='', simple=False):
"""Get the sections for a gradebook.
Return a dictionary of types of sections containing a list of that
type for a given gradebook. Specified by a gradebookid.
If simple=True, a list of dictionaries is provided for each
section regardless of type. The dictionary only contains one
key ``SectionName``.
Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
simple (bool): return a list of section names only
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
dict: Dictionary of section types where each type has a
list of sections
An example return value is:
.. code-block:: python
{
u'recitation':
[
{
u'editable': False,
u'groupId': 1293925,
u'groupingScheme': u'Recitation',
u'members': None,
u'name': u'Unassigned',
u'shortName': u'DefaultGroupNoCollisionPlease1234',
u'staffs': None
},
{
u'editable': True,
u'groupId': 1327565,
u'groupingScheme': u'Recitation',
u'members': None,
u'name': u'r01',
u'shortName': u'r01',
u'staffs': None},
{u'editable': True,
u'groupId': 1327555,
u'groupingScheme': u'Recitation',
u'members': None,
u'name': u'r02',
u'shortName': u'r02',
u'staffs': None
}
]
}
"""
params = dict(includeMembers='false')
section_data = self.get(
'sections/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
params=params
)
if simple:
sections = self.unravel_sections(section_data['data'])
return [{'SectionName': x['name']} for x in sections]
return section_data['data'] | python | def get_sections(self, gradebook_id='', simple=False):
params = dict(includeMembers='false')
section_data = self.get(
'sections/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
params=params
)
if simple:
sections = self.unravel_sections(section_data['data'])
return [{'SectionName': x['name']} for x in sections]
return section_data['data'] | [
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Return a dictionary of types of sections containing a list of that
type for a given gradebook. Specified by a gradebookid.
If simple=True, a list of dictionaries is provided for each
section regardless of type. The dictionary only contains one
key ``SectionName``.
Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
simple (bool): return a list of section names only
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
dict: Dictionary of section types where each type has a
list of sections
An example return value is:
.. code-block:: python
{
u'recitation':
[
{
u'editable': False,
u'groupId': 1293925,
u'groupingScheme': u'Recitation',
u'members': None,
u'name': u'Unassigned',
u'shortName': u'DefaultGroupNoCollisionPlease1234',
u'staffs': None
},
{
u'editable': True,
u'groupId': 1327565,
u'groupingScheme': u'Recitation',
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{u'editable': True,
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u'groupingScheme': u'Recitation',
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u'staffs': None
}
]
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] | b798b86c33d1eb615e7cd4f3457b5c15da1d86e0 | https://github.com/mitodl/PyLmod/blob/b798b86c33d1eb615e7cd4f3457b5c15da1d86e0/pylmod/gradebook.py#L611-L681 |
6,749 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.get_section_by_name | def get_section_by_name(self, section_name):
"""Get a section by its name.
Get a list of sections for a given gradebook,
specified by a gradebookid.
Args:
section_name (str): The section's name.
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
tuple: tuple of group id, and section dictionary
An example return value is:
.. code-block:: python
(
1327565,
{
u'editable': True,
u'groupId': 1327565,
u'groupingScheme': u'Recitation',
u'members': None,
u'name': u'r01',
u'shortName': u'r01',
u'staffs': None
}
)
"""
sections = self.unravel_sections(self.get_sections())
for section in sections:
if section['name'] == section_name:
return section['groupId'], section
return None, None | python | def get_section_by_name(self, section_name):
sections = self.unravel_sections(self.get_sections())
for section in sections:
if section['name'] == section_name:
return section['groupId'], section
return None, None | [
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Get a list of sections for a given gradebook,
specified by a gradebookid.
Args:
section_name (str): The section's name.
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
tuple: tuple of group id, and section dictionary
An example return value is:
.. code-block:: python
(
1327565,
{
u'editable': True,
u'groupId': 1327565,
u'groupingScheme': u'Recitation',
u'members': None,
u'name': u'r01',
u'shortName': u'r01',
u'staffs': None
}
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6,750 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.get_students | def get_students(
self,
gradebook_id='',
simple=False,
section_name='',
include_photo=False,
include_grade_info=False,
include_grade_history=False,
include_makeup_grades=False
):
"""Get students for a gradebook.
Get a list of students for a given gradebook,
specified by a gradebook id. Does not include grade data.
Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
simple (bool):
if ``True``, just return dictionary with keys ``email``,
``name``, ``section``, default = ``False``
section_name (str): section name
include_photo (bool): include student photo, default= ``False``
include_grade_info (bool):
include student's grade info, default= ``False``
include_grade_history (bool):
include student's grade history, default= ``False``
include_makeup_grades (bool):
include student's makeup grades, default= ``False``
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: list of student dictionaries
.. code-block:: python
[{
u'accountEmail': u'stellar.test2@gmail.com',
u'displayName': u'Molly Parker',
u'photoUrl': None,
u'middleName': None,
u'section': u'Unassigned',
u'sectionId': 1293925,
u'editable': False,
u'overallGradeInformation': None,
u'studentId': 1145,
u'studentAssignmentInfo': None,
u'sortableName': u'Parker, Molly',
u'surname': u'Parker',
u'givenName': u'Molly',
u'nickName': u'Molly',
u'email': u'stellar.test2@gmail.com'
},]
"""
# These are parameters required for the remote API call, so
# there aren't too many arguments, or too many variables
# pylint: disable=too-many-arguments,too-many-locals
# Set params by arguments
params = dict(
includePhoto=json.dumps(include_photo),
includeGradeInfo=json.dumps(include_grade_info),
includeGradeHistory=json.dumps(include_grade_history),
includeMakeupGrades=json.dumps(include_makeup_grades),
)
url = 'students/{gradebookId}'
if section_name:
group_id, _ = self.get_section_by_name(section_name)
if group_id is None:
failure_message = (
'in get_students -- Error: '
'No such section %s' % section_name
)
log.critical(failure_message)
raise PyLmodNoSuchSection(failure_message)
url += '/section/{0}'.format(group_id)
student_data = self.get(
url.format(
gradebookId=gradebook_id or self.gradebook_id
),
params=params,
)
if simple:
# just return dict with keys email, name, section
student_map = dict(
accountEmail='email',
displayName='name',
section='section'
)
def remap(students):
"""Convert mit.edu domain to upper-case for student emails.
The mit.edu domain for user email must be upper-case,
i.e. MIT.EDU.
Args:
students (list): list of students
Returns:
dict: dictionary of updated student email domains
"""
newx = dict((student_map[k], students[k]) for k in student_map)
# match certs
newx['email'] = newx['email'].replace('@mit.edu', '@MIT.EDU')
return newx
return [remap(x) for x in student_data['data']]
return student_data['data'] | python | def get_students(
self,
gradebook_id='',
simple=False,
section_name='',
include_photo=False,
include_grade_info=False,
include_grade_history=False,
include_makeup_grades=False
):
# These are parameters required for the remote API call, so
# there aren't too many arguments, or too many variables
# pylint: disable=too-many-arguments,too-many-locals
# Set params by arguments
params = dict(
includePhoto=json.dumps(include_photo),
includeGradeInfo=json.dumps(include_grade_info),
includeGradeHistory=json.dumps(include_grade_history),
includeMakeupGrades=json.dumps(include_makeup_grades),
)
url = 'students/{gradebookId}'
if section_name:
group_id, _ = self.get_section_by_name(section_name)
if group_id is None:
failure_message = (
'in get_students -- Error: '
'No such section %s' % section_name
)
log.critical(failure_message)
raise PyLmodNoSuchSection(failure_message)
url += '/section/{0}'.format(group_id)
student_data = self.get(
url.format(
gradebookId=gradebook_id or self.gradebook_id
),
params=params,
)
if simple:
# just return dict with keys email, name, section
student_map = dict(
accountEmail='email',
displayName='name',
section='section'
)
def remap(students):
"""Convert mit.edu domain to upper-case for student emails.
The mit.edu domain for user email must be upper-case,
i.e. MIT.EDU.
Args:
students (list): list of students
Returns:
dict: dictionary of updated student email domains
"""
newx = dict((student_map[k], students[k]) for k in student_map)
# match certs
newx['email'] = newx['email'].replace('@mit.edu', '@MIT.EDU')
return newx
return [remap(x) for x in student_data['data']]
return student_data['data'] | [
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Get a list of students for a given gradebook,
specified by a gradebook id. Does not include grade data.
Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
simple (bool):
if ``True``, just return dictionary with keys ``email``,
``name``, ``section``, default = ``False``
section_name (str): section name
include_photo (bool): include student photo, default= ``False``
include_grade_info (bool):
include student's grade info, default= ``False``
include_grade_history (bool):
include student's grade history, default= ``False``
include_makeup_grades (bool):
include student's makeup grades, default= ``False``
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: list of student dictionaries
.. code-block:: python
[{
u'accountEmail': u'stellar.test2@gmail.com',
u'displayName': u'Molly Parker',
u'photoUrl': None,
u'middleName': None,
u'section': u'Unassigned',
u'sectionId': 1293925,
u'editable': False,
u'overallGradeInformation': None,
u'studentId': 1145,
u'studentAssignmentInfo': None,
u'sortableName': u'Parker, Molly',
u'surname': u'Parker',
u'givenName': u'Molly',
u'nickName': u'Molly',
u'email': u'stellar.test2@gmail.com'
},] | [
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"."
] | b798b86c33d1eb615e7cd4f3457b5c15da1d86e0 | https://github.com/mitodl/PyLmod/blob/b798b86c33d1eb615e7cd4f3457b5c15da1d86e0/pylmod/gradebook.py#L723-L838 |
6,751 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.get_student_by_email | def get_student_by_email(self, email, students=None):
"""Get a student based on an email address.
Calls ``self.get_students()`` to get list of all students,
if not passed as the ``students`` parameter.
Args:
email (str): student email
students (list): dictionary of students to search, default: None
When ``students`` is unspecified, all students in gradebook
are retrieved.
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
tuple: tuple of student id and student dictionary.
"""
if students is None:
students = self.get_students()
email = email.lower()
for student in students:
if student['accountEmail'].lower() == email:
return student['studentId'], student
return None, None | python | def get_student_by_email(self, email, students=None):
if students is None:
students = self.get_students()
email = email.lower()
for student in students:
if student['accountEmail'].lower() == email:
return student['studentId'], student
return None, None | [
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Calls ``self.get_students()`` to get list of all students,
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Args:
email (str): student email
students (list): dictionary of students to search, default: None
When ``students`` is unspecified, all students in gradebook
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Raises:
requests.RequestException: Exception connection error
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Returns:
tuple: tuple of student id and student dictionary. | [
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6,752 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.spreadsheet2gradebook | def spreadsheet2gradebook(
self,
csv_file,
email_field=None,
approve_grades=False,
use_max_points_column=False,
max_points_column=None,
normalize_column=None
):
"""Upload grade spreadsheet to gradebook.
Upload grades from CSV format spreadsheet file into the
Learning Modules gradebook. The spreadsheet must have a column
named ``External email`` which is used as the student's email
address (for looking up and matching studentId).
These columns are disregarded: ``ID``, ``Username``,
``Full Name``, ``edX email``, ``External email``,
as well as the strings passed in ``max_points_column``
and ``normalize_column``, if any.
All other columns are taken as assignments.
If ``email_field`` is specified, then that field name is taken as
the student's email.
.. code-block:: none
External email,AB Assignment 01,AB Assignment 02
jeannechiang@gmail.com,1.0,0.9
stellar.test2@gmail.com,0.2,0.4
stellar.test1@gmail.com,0.93,0.77
Args:
csv_reader (str): filename of csv data, or readable file object
email_field (str): student's email
approve_grades (bool): Should grades be auto approved?
use_max_points_column (bool):
If ``True``, read the max points and normalize values
from the CSV and use the max points value in place of
the default if normalized is ``False``.
max_points_column (str): The name of the max_pts column. All
rows contain the same number, the max points for
the assignment.
normalize_column (str): The name of the normalize column which
indicates whether to use the max points value.
Raises:
PyLmodFailedAssignmentCreation: Failed to create assignment
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
tuple: tuple of dictionary containing response ``status``
and ``message``, and duration of operation
"""
non_assignment_fields = [
'ID', 'Username', 'Full Name', 'edX email', 'External email'
]
if max_points_column is not None:
non_assignment_fields.append(max_points_column)
if normalize_column is not None:
non_assignment_fields.append(normalize_column)
if email_field is not None:
non_assignment_fields.append(email_field)
else:
email_field = 'External email'
if not hasattr(csv_file, 'read'):
file_pointer = open(csv_file)
else:
file_pointer = csv_file
csv_reader = csv.DictReader(file_pointer, dialect='excel')
response = self._spreadsheet2gradebook_multi(
csv_reader,
email_field,
non_assignment_fields,
approve_grades=approve_grades,
use_max_points_column=use_max_points_column,
max_points_column=max_points_column,
normalize_column=normalize_column
)
return response | python | def spreadsheet2gradebook(
self,
csv_file,
email_field=None,
approve_grades=False,
use_max_points_column=False,
max_points_column=None,
normalize_column=None
):
non_assignment_fields = [
'ID', 'Username', 'Full Name', 'edX email', 'External email'
]
if max_points_column is not None:
non_assignment_fields.append(max_points_column)
if normalize_column is not None:
non_assignment_fields.append(normalize_column)
if email_field is not None:
non_assignment_fields.append(email_field)
else:
email_field = 'External email'
if not hasattr(csv_file, 'read'):
file_pointer = open(csv_file)
else:
file_pointer = csv_file
csv_reader = csv.DictReader(file_pointer, dialect='excel')
response = self._spreadsheet2gradebook_multi(
csv_reader,
email_field,
non_assignment_fields,
approve_grades=approve_grades,
use_max_points_column=use_max_points_column,
max_points_column=max_points_column,
normalize_column=normalize_column
)
return response | [
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Upload grades from CSV format spreadsheet file into the
Learning Modules gradebook. The spreadsheet must have a column
named ``External email`` which is used as the student's email
address (for looking up and matching studentId).
These columns are disregarded: ``ID``, ``Username``,
``Full Name``, ``edX email``, ``External email``,
as well as the strings passed in ``max_points_column``
and ``normalize_column``, if any.
All other columns are taken as assignments.
If ``email_field`` is specified, then that field name is taken as
the student's email.
.. code-block:: none
External email,AB Assignment 01,AB Assignment 02
jeannechiang@gmail.com,1.0,0.9
stellar.test2@gmail.com,0.2,0.4
stellar.test1@gmail.com,0.93,0.77
Args:
csv_reader (str): filename of csv data, or readable file object
email_field (str): student's email
approve_grades (bool): Should grades be auto approved?
use_max_points_column (bool):
If ``True``, read the max points and normalize values
from the CSV and use the max points value in place of
the default if normalized is ``False``.
max_points_column (str): The name of the max_pts column. All
rows contain the same number, the max points for
the assignment.
normalize_column (str): The name of the normalize column which
indicates whether to use the max points value.
Raises:
PyLmodFailedAssignmentCreation: Failed to create assignment
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
tuple: tuple of dictionary containing response ``status``
and ``message``, and duration of operation | [
"Upload",
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] | b798b86c33d1eb615e7cd4f3457b5c15da1d86e0 | https://github.com/mitodl/PyLmod/blob/b798b86c33d1eb615e7cd4f3457b5c15da1d86e0/pylmod/gradebook.py#L1053-L1137 |
6,753 | mitodl/PyLmod | pylmod/gradebook.py | GradeBook.get_staff | def get_staff(self, gradebook_id, simple=False):
"""Get staff list for gradebook.
Get staff list for the gradebook specified. Optionally, return
a less detailed list by specifying ``simple = True``.
If simple=True, return a list of dictionaries, one dictionary
for each member. The dictionary contains a member's ``email``,
``displayName``, and ``role``. Members with multiple roles will
appear in the list once for each role.
Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
simple (bool): Return a staff list with less detail. Default
is ``False``.
Returns:
An example return value is:
.. code-block:: python
{
u'data': {
u'COURSE_ADMIN': [
{
u'accountEmail': u'benfranklin@mit.edu',
u'displayName': u'Benjamin Franklin',
u'editable': False,
u'email': u'benfranklin@mit.edu',
u'givenName': u'Benjamin',
u'middleName': None,
u'mitId': u'921344431',
u'nickName': u'Benjamin',
u'personId': 10710616,
u'sortableName': u'Franklin, Benjamin',
u'surname': u'Franklin',
u'year': None
},
],
u'COURSE_PROF': [
{
u'accountEmail': u'dduck@mit.edu',
u'displayName': u'Donald Duck',
u'editable': False,
u'email': u'dduck@mit.edu',
u'givenName': u'Donald',
u'middleName': None,
u'mitId': u'916144889',
u'nickName': u'Donald',
u'personId': 8117160,
u'sortableName': u'Duck, Donald',
u'surname': u'Duck',
u'year': None
},
],
u'COURSE_TA': [
{
u'accountEmail': u'hduck@mit.edu',
u'displayName': u'Huey Duck',
u'editable': False,
u'email': u'hduck@mit.edu',
u'givenName': u'Huey',
u'middleName': None,
u'mitId': u'920445024',
u'nickName': u'Huey',
u'personId': 1299059,
u'sortableName': u'Duck, Huey',
u'surname': u'Duck',
u'year': None
},
]
},
}
"""
staff_data = self.get(
'staff/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
params=None,
)
if simple:
simple_list = []
unraveled_list = self.unravel_staff(staff_data)
for member in unraveled_list.__iter__():
simple_list.append({
'accountEmail': member['accountEmail'],
'displayName': member['displayName'],
'role': member['role'],
})
return simple_list
return staff_data['data'] | python | def get_staff(self, gradebook_id, simple=False):
staff_data = self.get(
'staff/{gradebookId}'.format(
gradebookId=gradebook_id or self.gradebook_id
),
params=None,
)
if simple:
simple_list = []
unraveled_list = self.unravel_staff(staff_data)
for member in unraveled_list.__iter__():
simple_list.append({
'accountEmail': member['accountEmail'],
'displayName': member['displayName'],
'role': member['role'],
})
return simple_list
return staff_data['data'] | [
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Get staff list for the gradebook specified. Optionally, return
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for each member. The dictionary contains a member's ``email``,
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Args:
gradebook_id (str): unique identifier for gradebook, i.e. ``2314``
simple (bool): Return a staff list with less detail. Default
is ``False``.
Returns:
An example return value is:
.. code-block:: python
{
u'data': {
u'COURSE_ADMIN': [
{
u'accountEmail': u'benfranklin@mit.edu',
u'displayName': u'Benjamin Franklin',
u'editable': False,
u'email': u'benfranklin@mit.edu',
u'givenName': u'Benjamin',
u'middleName': None,
u'mitId': u'921344431',
u'nickName': u'Benjamin',
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u'surname': u'Franklin',
u'year': None
},
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u'accountEmail': u'dduck@mit.edu',
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u'editable': False,
u'email': u'dduck@mit.edu',
u'givenName': u'Donald',
u'middleName': None,
u'mitId': u'916144889',
u'nickName': u'Donald',
u'personId': 8117160,
u'sortableName': u'Duck, Donald',
u'surname': u'Duck',
u'year': None
},
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u'COURSE_TA': [
{
u'accountEmail': u'hduck@mit.edu',
u'displayName': u'Huey Duck',
u'editable': False,
u'email': u'hduck@mit.edu',
u'givenName': u'Huey',
u'middleName': None,
u'mitId': u'920445024',
u'nickName': u'Huey',
u'personId': 1299059,
u'sortableName': u'Duck, Huey',
u'surname': u'Duck',
u'year': None
},
]
},
} | [
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6,754 | mitodl/PyLmod | pylmod/membership.py | Membership.get_group | def get_group(self, uuid=None):
"""Get group data based on uuid.
Args:
uuid (str): optional uuid. defaults to self.cuuid
Raises:
PyLmodUnexpectedData: No data was returned.
requests.RequestException: Exception connection error
Returns:
dict: group json
"""
if uuid is None:
uuid = self.uuid
group_data = self.get('group', params={'uuid': uuid})
return group_data | python | def get_group(self, uuid=None):
if uuid is None:
uuid = self.uuid
group_data = self.get('group', params={'uuid': uuid})
return group_data | [
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Returns:
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6,755 | mitodl/PyLmod | pylmod/membership.py | Membership.get_group_id | def get_group_id(self, uuid=None):
"""Get group id based on uuid.
Args:
uuid (str): optional uuid. defaults to self.cuuid
Raises:
PyLmodUnexpectedData: No group data was returned.
requests.RequestException: Exception connection error
Returns:
int: numeric group id
"""
group_data = self.get_group(uuid)
try:
return group_data['response']['docs'][0]['id']
except (KeyError, IndexError):
failure_message = ('Error in get_group response data - '
'got {0}'.format(group_data))
log.exception(failure_message)
raise PyLmodUnexpectedData(failure_message) | python | def get_group_id(self, uuid=None):
group_data = self.get_group(uuid)
try:
return group_data['response']['docs'][0]['id']
except (KeyError, IndexError):
failure_message = ('Error in get_group response data - '
'got {0}'.format(group_data))
log.exception(failure_message)
raise PyLmodUnexpectedData(failure_message) | [
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requests.RequestException: Exception connection error
Returns:
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6,756 | mitodl/PyLmod | pylmod/membership.py | Membership.get_membership | def get_membership(self, uuid=None):
"""Get membership data based on uuid.
Args:
uuid (str): optional uuid. defaults to self.cuuid
Raises:
PyLmodUnexpectedData: No data was returned.
requests.RequestException: Exception connection error
Returns:
dict: membership json
"""
group_id = self.get_group_id(uuid=uuid)
uri = 'group/{group_id}/member'
mbr_data = self.get(uri.format(group_id=group_id), params=None)
return mbr_data | python | def get_membership(self, uuid=None):
group_id = self.get_group_id(uuid=uuid)
uri = 'group/{group_id}/member'
mbr_data = self.get(uri.format(group_id=group_id), params=None)
return mbr_data | [
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6,757 | mitodl/PyLmod | pylmod/membership.py | Membership.email_has_role | def email_has_role(self, email, role_name, uuid=None):
"""Determine if an email is associated with a role.
Args:
email (str): user email
role_name (str): user role
uuid (str): optional uuid. defaults to self.cuuid
Raises:
PyLmodUnexpectedData: Unexpected data was returned.
requests.RequestException: Exception connection error
Returns:
bool: True or False if email has role_name
"""
mbr_data = self.get_membership(uuid=uuid)
docs = []
try:
docs = mbr_data['response']['docs']
except KeyError:
failure_message = ('KeyError in membership data - '
'got {0}'.format(mbr_data))
log.exception(failure_message)
raise PyLmodUnexpectedData(failure_message)
if len(docs) == 0:
return False
has_role = any(
(x.get('email') == email and x.get('roleType') == role_name)
for x in docs
)
if has_role:
return True
return False | python | def email_has_role(self, email, role_name, uuid=None):
mbr_data = self.get_membership(uuid=uuid)
docs = []
try:
docs = mbr_data['response']['docs']
except KeyError:
failure_message = ('KeyError in membership data - '
'got {0}'.format(mbr_data))
log.exception(failure_message)
raise PyLmodUnexpectedData(failure_message)
if len(docs) == 0:
return False
has_role = any(
(x.get('email') == email and x.get('roleType') == role_name)
for x in docs
)
if has_role:
return True
return False | [
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uuid (str): optional uuid. defaults to self.cuuid
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6,758 | mitodl/PyLmod | pylmod/membership.py | Membership.get_course_id | def get_course_id(self, course_uuid):
"""Get course id based on uuid.
Args:
uuid (str): course uuid, i.e. /project/mitxdemosite
Raises:
PyLmodUnexpectedData: No course data was returned.
requests.RequestException: Exception connection error
Returns:
int: numeric course id
"""
course_data = self.get(
'courseguide/course?uuid={uuid}'.format(
uuid=course_uuid or self.course_id
),
params=None
)
try:
return course_data['response']['docs'][0]['id']
except KeyError:
failure_message = ('KeyError in get_course_id - '
'got {0}'.format(course_data))
log.exception(failure_message)
raise PyLmodUnexpectedData(failure_message)
except TypeError:
failure_message = ('TypeError in get_course_id - '
'got {0}'.format(course_data))
log.exception(failure_message)
raise PyLmodUnexpectedData(failure_message) | python | def get_course_id(self, course_uuid):
course_data = self.get(
'courseguide/course?uuid={uuid}'.format(
uuid=course_uuid or self.course_id
),
params=None
)
try:
return course_data['response']['docs'][0]['id']
except KeyError:
failure_message = ('KeyError in get_course_id - '
'got {0}'.format(course_data))
log.exception(failure_message)
raise PyLmodUnexpectedData(failure_message)
except TypeError:
failure_message = ('TypeError in get_course_id - '
'got {0}'.format(course_data))
log.exception(failure_message)
raise PyLmodUnexpectedData(failure_message) | [
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6,759 | mitodl/PyLmod | pylmod/membership.py | Membership.get_course_guide_staff | def get_course_guide_staff(self, course_id=''):
"""Get the staff roster for a course.
Get a list of staff members for a given course,
specified by a course id.
Args:
course_id (int): unique identifier for course, i.e. ``2314``
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: list of dictionaries containing staff data
An example return value is:
.. code-block:: python
[
{
u'displayName': u'Huey Duck',
u'role': u'TA',
u'sortableDisplayName': u'Duck, Huey'
},
{
u'displayName': u'Louie Duck',
u'role': u'CourseAdmin',
u'sortableDisplayName': u'Duck, Louie'
},
{
u'displayName': u'Benjamin Franklin',
u'role': u'CourseAdmin',
u'sortableDisplayName': u'Franklin, Benjamin'
},
{
u'displayName': u'George Washington',
u'role': u'Instructor',
u'sortableDisplayName': u'Washington, George'
},
]
"""
staff_data = self.get(
'courseguide/course/{courseId}/staff'.format(
courseId=course_id or self.course_id
),
params=None
)
return staff_data['response']['docs'] | python | def get_course_guide_staff(self, course_id=''):
staff_data = self.get(
'courseguide/course/{courseId}/staff'.format(
courseId=course_id or self.course_id
),
params=None
)
return staff_data['response']['docs'] | [
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Raises:
requests.RequestException: Exception connection error
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Returns:
list: list of dictionaries containing staff data
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.. code-block:: python
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u'displayName': u'Huey Duck',
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{
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6,760 | mitodl/PyLmod | pylmod/base.py | Base._data_to_json | def _data_to_json(data):
"""Convert to json if it isn't already a string.
Args:
data (str): data to convert to json
"""
if type(data) not in [str, unicode]:
data = json.dumps(data)
return data | python | def _data_to_json(data):
if type(data) not in [str, unicode]:
data = json.dumps(data)
return data | [
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6,761 | mitodl/PyLmod | pylmod/base.py | Base._url_format | def _url_format(self, service):
"""Generate URL from urlbase and service.
Args:
service (str): The endpoint service to use, i.e. gradebook
Returns:
str: URL to where the request should be made
"""
base_service_url = '{base}{service}'.format(
base=self.urlbase,
service=service
)
return base_service_url | python | def _url_format(self, service):
base_service_url = '{base}{service}'.format(
base=self.urlbase,
service=service
)
return base_service_url | [
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6,762 | mitodl/PyLmod | pylmod/base.py | Base.rest_action | def rest_action(self, func, url, **kwargs):
"""Routine to do low-level REST operation, with retry.
Args:
func (callable): API function to call
url (str): service URL endpoint
kwargs (dict): addition parameters
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: the json-encoded content of the response
"""
try:
response = func(url, timeout=self.TIMEOUT, **kwargs)
except requests.RequestException, err:
log.exception(
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"rest_action, err=%s", err
)
raise err
try:
return response.json()
except ValueError, err:
log.exception('Unable to decode %s', response.content)
raise err | python | def rest_action(self, func, url, **kwargs):
try:
response = func(url, timeout=self.TIMEOUT, **kwargs)
except requests.RequestException, err:
log.exception(
"[PyLmod] Error - connection error in "
"rest_action, err=%s", err
)
raise err
try:
return response.json()
except ValueError, err:
log.exception('Unable to decode %s', response.content)
raise err | [
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6,763 | mitodl/PyLmod | pylmod/base.py | Base.get | def get(self, service, params=None):
"""Generic GET operation for retrieving data from Learning Modules API.
.. code-block:: python
gbk.get('students/{gradebookId}', params=params, gradebookId=gbid)
Args:
service (str): The endpoint service to use, i.e. gradebook
params (dict): additional parameters to add to the call
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: the json-encoded content of the response
"""
url = self._url_format(service)
if params is None:
params = {}
return self.rest_action(self._session.get, url, params=params) | python | def get(self, service, params=None):
url = self._url_format(service)
if params is None:
params = {}
return self.rest_action(self._session.get, url, params=params) | [
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6,764 | mitodl/PyLmod | pylmod/base.py | Base.post | def post(self, service, data):
"""Generic POST operation for sending data to Learning Modules API.
Data should be a JSON string or a dict. If it is not a string,
it is turned into a JSON string for the POST body.
Args:
service (str): The endpoint service to use, i.e. gradebook
data (json or dict): the data payload
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: the json-encoded content of the response
"""
url = self._url_format(service)
data = Base._data_to_json(data)
# Add content-type for body in POST.
headers = {'content-type': 'application/json'}
return self.rest_action(self._session.post, url,
data=data, headers=headers) | python | def post(self, service, data):
url = self._url_format(service)
data = Base._data_to_json(data)
# Add content-type for body in POST.
headers = {'content-type': 'application/json'}
return self.rest_action(self._session.post, url,
data=data, headers=headers) | [
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6,765 | mitodl/PyLmod | pylmod/base.py | Base.delete | def delete(self, service):
"""Generic DELETE operation for Learning Modules API.
Args:
service (str): The endpoint service to use, i.e. gradebook
Raises:
requests.RequestException: Exception connection error
ValueError: Unable to decode response content
Returns:
list: the json-encoded content of the response
"""
url = self._url_format(service)
return self.rest_action(
self._session.delete, url
) | python | def delete(self, service):
url = self._url_format(service)
return self.rest_action(
self._session.delete, url
) | [
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6,766 | jmcarp/sqlalchemy-postgres-copy | postgres_copy/__init__.py | raw_connection_from | def raw_connection_from(engine_or_conn):
"""Extract a raw_connection and determine if it should be automatically closed.
Only connections opened by this package will be closed automatically.
"""
if hasattr(engine_or_conn, 'cursor'):
return engine_or_conn, False
if hasattr(engine_or_conn, 'connection'):
return engine_or_conn.connection, False
return engine_or_conn.raw_connection(), True | python | def raw_connection_from(engine_or_conn):
if hasattr(engine_or_conn, 'cursor'):
return engine_or_conn, False
if hasattr(engine_or_conn, 'connection'):
return engine_or_conn.connection, False
return engine_or_conn.raw_connection(), True | [
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6,767 | biocommons/biocommons.seqrepo | biocommons/seqrepo/py2compat/_makedirs.py | makedirs | def makedirs(name, mode=0o777, exist_ok=False):
"""cheapo replacement for py3 makedirs with support for exist_ok
"""
if os.path.exists(name):
if not exist_ok:
raise FileExistsError("File exists: " + name)
else:
os.makedirs(name, mode) | python | def makedirs(name, mode=0o777, exist_ok=False):
if os.path.exists(name):
if not exist_ok:
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else:
os.makedirs(name, mode) | [
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6,768 | biocommons/biocommons.seqrepo | misc/threading-verification.py | fetch_in_thread | def fetch_in_thread(sr, nsa):
"""fetch a sequence in a thread
"""
def fetch_seq(q, nsa):
pid, ppid = os.getpid(), os.getppid()
q.put((pid, ppid, sr[nsa]))
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p.start()
pid, ppid, seq = q.get()
p.join()
assert pid != ppid, "sequence was not fetched from thread"
return pid, ppid, seq | python | def fetch_in_thread(sr, nsa):
def fetch_seq(q, nsa):
pid, ppid = os.getpid(), os.getppid()
q.put((pid, ppid, sr[nsa]))
q = Queue()
p = Process(target=fetch_seq, args=(q, nsa))
p.start()
pid, ppid, seq = q.get()
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6,769 | junaruga/rpm-py-installer | install.py | Application.run | def run(self):
"""Run install process."""
try:
self.linux.verify_system_status()
except InstallSkipError:
Log.info('Install skipped.')
return
work_dir = tempfile.mkdtemp(suffix='-rpm-py-installer')
Log.info("Created working directory '{0}'".format(work_dir))
with Cmd.pushd(work_dir):
self.rpm_py.download_and_install()
if not self.python.is_python_binding_installed():
message = (
'RPM Python binding failed to install '
'with unknown reason.'
)
raise InstallError(message)
# TODO: Print installed module name and version as INFO.
if self.is_work_dir_removed:
shutil.rmtree(work_dir)
Log.info("Removed working directory '{0}'".format(work_dir))
else:
Log.info("Saved working directory '{0}'".format(work_dir)) | python | def run(self):
try:
self.linux.verify_system_status()
except InstallSkipError:
Log.info('Install skipped.')
return
work_dir = tempfile.mkdtemp(suffix='-rpm-py-installer')
Log.info("Created working directory '{0}'".format(work_dir))
with Cmd.pushd(work_dir):
self.rpm_py.download_and_install()
if not self.python.is_python_binding_installed():
message = (
'RPM Python binding failed to install '
'with unknown reason.'
)
raise InstallError(message)
# TODO: Print installed module name and version as INFO.
if self.is_work_dir_removed:
shutil.rmtree(work_dir)
Log.info("Removed working directory '{0}'".format(work_dir))
else:
Log.info("Saved working directory '{0}'".format(work_dir)) | [
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6,770 | junaruga/rpm-py-installer | install.py | RpmPy.download_and_install | def download_and_install(self):
"""Download and install RPM Python binding."""
if self.is_installed_from_bin:
try:
self.installer.install_from_rpm_py_package()
return
except RpmPyPackageNotFoundError as e:
Log.warn('RPM Py Package not found. reason: {0}'.format(e))
# Pass to try to install from the source.
pass
# Download and install from the source.
top_dir_name = self.downloader.download_and_expand()
rpm_py_dir = os.path.join(top_dir_name, 'python')
setup_py_in_found = False
with Cmd.pushd(rpm_py_dir):
if self.installer.setup_py.exists_in_path():
setup_py_in_found = True
self.installer.run()
if not setup_py_in_found:
self.installer.install_from_rpm_py_package() | python | def download_and_install(self):
if self.is_installed_from_bin:
try:
self.installer.install_from_rpm_py_package()
return
except RpmPyPackageNotFoundError as e:
Log.warn('RPM Py Package not found. reason: {0}'.format(e))
# Pass to try to install from the source.
pass
# Download and install from the source.
top_dir_name = self.downloader.download_and_expand()
rpm_py_dir = os.path.join(top_dir_name, 'python')
setup_py_in_found = False
with Cmd.pushd(rpm_py_dir):
if self.installer.setup_py.exists_in_path():
setup_py_in_found = True
self.installer.run()
if not setup_py_in_found:
self.installer.install_from_rpm_py_package() | [
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6,771 | junaruga/rpm-py-installer | install.py | RpmPyVersion.git_branch | def git_branch(self):
"""Git branch name."""
info = self.info
return 'rpm-{major}.{minor}.x'.format(
major=info[0], minor=info[1]) | python | def git_branch(self):
info = self.info
return 'rpm-{major}.{minor}.x'.format(
major=info[0], minor=info[1]) | [
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6,772 | junaruga/rpm-py-installer | install.py | SetupPy.add_patchs_to_build_without_pkg_config | def add_patchs_to_build_without_pkg_config(self, lib_dir, include_dir):
"""Add patches to remove pkg-config command and rpm.pc part.
Replace with given library_path: lib_dir and include_path: include_dir
without rpm.pc file.
"""
additional_patches = [
{
'src': r"pkgconfig\('--libs-only-L'\)",
'dest': "['{0}']".format(lib_dir),
},
# Considering -libs-only-l and -libs-only-L
# https://github.com/rpm-software-management/rpm/pull/327
{
'src': r"pkgconfig\('--libs(-only-l)?'\)",
'dest': "['rpm', 'rpmio']",
'required': True,
},
{
'src': r"pkgconfig\('--cflags'\)",
'dest': "['{0}']".format(include_dir),
'required': True,
},
]
self.patches.extend(additional_patches) | python | def add_patchs_to_build_without_pkg_config(self, lib_dir, include_dir):
additional_patches = [
{
'src': r"pkgconfig\('--libs-only-L'\)",
'dest': "['{0}']".format(lib_dir),
},
# Considering -libs-only-l and -libs-only-L
# https://github.com/rpm-software-management/rpm/pull/327
{
'src': r"pkgconfig\('--libs(-only-l)?'\)",
'dest': "['rpm', 'rpmio']",
'required': True,
},
{
'src': r"pkgconfig\('--cflags'\)",
'dest': "['{0}']".format(include_dir),
'required': True,
},
]
self.patches.extend(additional_patches) | [
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6,773 | junaruga/rpm-py-installer | install.py | SetupPy.apply_and_save | def apply_and_save(self):
"""Apply replaced words and patches, and save setup.py file."""
patches = self.patches
content = None
with open(self.IN_PATH) as f_in:
# As setup.py.in file size is 2.4 KByte.
# it's fine to read entire content.
content = f_in.read()
# Replace words.
for key in self.replaced_word_dict:
content = content.replace(key, self.replaced_word_dict[key])
# Apply patches.
out_patches = []
for patch in patches:
pattern = re.compile(patch['src'], re.MULTILINE)
(content, subs_num) = re.subn(pattern, patch['dest'],
content)
if subs_num > 0:
patch['applied'] = True
out_patches.append(patch)
for patch in out_patches:
if patch.get('required') and not patch.get('applied'):
Log.warn('Patch not applied {0}'.format(patch['src']))
with open(self.OUT_PATH, 'w') as f_out:
f_out.write(content)
self.pathces = out_patches
# Release content data to make it released by GC quickly.
content = None | python | def apply_and_save(self):
patches = self.patches
content = None
with open(self.IN_PATH) as f_in:
# As setup.py.in file size is 2.4 KByte.
# it's fine to read entire content.
content = f_in.read()
# Replace words.
for key in self.replaced_word_dict:
content = content.replace(key, self.replaced_word_dict[key])
# Apply patches.
out_patches = []
for patch in patches:
pattern = re.compile(patch['src'], re.MULTILINE)
(content, subs_num) = re.subn(pattern, patch['dest'],
content)
if subs_num > 0:
patch['applied'] = True
out_patches.append(patch)
for patch in out_patches:
if patch.get('required') and not patch.get('applied'):
Log.warn('Patch not applied {0}'.format(patch['src']))
with open(self.OUT_PATH, 'w') as f_out:
f_out.write(content)
self.pathces = out_patches
# Release content data to make it released by GC quickly.
content = None | [
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6,774 | junaruga/rpm-py-installer | install.py | Downloader.download_and_expand | def download_and_expand(self):
"""Download and expand RPM Python binding."""
top_dir_name = None
if self.git_branch:
# Download a source by git clone.
top_dir_name = self._download_and_expand_by_git()
else:
# Download a source from the arcihve URL.
# Downloading the compressed archive is better than "git clone",
# because it is faster.
# If download failed due to URL not found, try "git clone".
try:
top_dir_name = self._download_and_expand_from_archive_url()
except RemoteFileNotFoundError:
Log.info('Try to download by git clone.')
top_dir_name = self._download_and_expand_by_git()
return top_dir_name | python | def download_and_expand(self):
top_dir_name = None
if self.git_branch:
# Download a source by git clone.
top_dir_name = self._download_and_expand_by_git()
else:
# Download a source from the arcihve URL.
# Downloading the compressed archive is better than "git clone",
# because it is faster.
# If download failed due to URL not found, try "git clone".
try:
top_dir_name = self._download_and_expand_from_archive_url()
except RemoteFileNotFoundError:
Log.info('Try to download by git clone.')
top_dir_name = self._download_and_expand_by_git()
return top_dir_name | [
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6,775 | junaruga/rpm-py-installer | install.py | Installer._make_lib_file_symbolic_links | def _make_lib_file_symbolic_links(self):
"""Make symbolic links for lib files.
Make symbolic links from system library files or downloaded lib files
to downloaded source library files.
For example, case: Fedora x86_64
Make symbolic links
from
a. /usr/lib64/librpmio.so* (one of them)
b. /usr/lib64/librpm.so* (one of them)
c. If rpm-build-libs package is installed,
/usr/lib64/librpmbuild.so* (one of them)
otherwise, downloaded and extracted rpm-build-libs.
./usr/lib64/librpmbuild.so* (one of them)
c. If rpm-build-libs package is installed,
/usr/lib64/librpmsign.so* (one of them)
otherwise, downloaded and extracted rpm-build-libs.
./usr/lib64/librpmsign.so* (one of them)
to
a. rpm/rpmio/.libs/librpmio.so
b. rpm/lib/.libs/librpm.so
c. rpm/build/.libs/librpmbuild.so
d. rpm/sign/.libs/librpmsign.so
.
This is a status after running "make" on actual rpm build process.
"""
so_file_dict = {
'rpmio': {
'sym_src_dir': self.rpm.lib_dir,
'sym_dst_dir': 'rpmio/.libs',
'require': True,
},
'rpm': {
'sym_src_dir': self.rpm.lib_dir,
'sym_dst_dir': 'lib/.libs',
'require': True,
},
'rpmbuild': {
'sym_src_dir': self.rpm.lib_dir,
'sym_dst_dir': 'build/.libs',
'require': True,
},
'rpmsign': {
'sym_src_dir': self.rpm.lib_dir,
'sym_dst_dir': 'sign/.libs',
},
}
self._update_sym_src_dirs_conditionally(so_file_dict)
for name in so_file_dict:
so_dict = so_file_dict[name]
pattern = 'lib{0}.so*'.format(name)
so_files = Cmd.find(so_dict['sym_src_dir'], pattern)
if not so_files:
is_required = so_dict.get('require', False)
if not is_required:
message_format = (
"Skip creating symbolic link of "
"not existing so file '{0}'"
)
Log.debug(message_format.format(name))
continue
message = 'so file pattern {0} not found at {1}'.format(
pattern, so_dict['sym_src_dir']
)
raise InstallError(message)
sym_dst_dir = os.path.abspath('../{0}'.format(
so_dict['sym_dst_dir']))
if not os.path.isdir(sym_dst_dir):
Cmd.mkdir_p(sym_dst_dir)
cmd = 'ln -sf {0} {1}/lib{2}.so'.format(so_files[0],
sym_dst_dir,
name)
Cmd.sh_e(cmd) | python | def _make_lib_file_symbolic_links(self):
so_file_dict = {
'rpmio': {
'sym_src_dir': self.rpm.lib_dir,
'sym_dst_dir': 'rpmio/.libs',
'require': True,
},
'rpm': {
'sym_src_dir': self.rpm.lib_dir,
'sym_dst_dir': 'lib/.libs',
'require': True,
},
'rpmbuild': {
'sym_src_dir': self.rpm.lib_dir,
'sym_dst_dir': 'build/.libs',
'require': True,
},
'rpmsign': {
'sym_src_dir': self.rpm.lib_dir,
'sym_dst_dir': 'sign/.libs',
},
}
self._update_sym_src_dirs_conditionally(so_file_dict)
for name in so_file_dict:
so_dict = so_file_dict[name]
pattern = 'lib{0}.so*'.format(name)
so_files = Cmd.find(so_dict['sym_src_dir'], pattern)
if not so_files:
is_required = so_dict.get('require', False)
if not is_required:
message_format = (
"Skip creating symbolic link of "
"not existing so file '{0}'"
)
Log.debug(message_format.format(name))
continue
message = 'so file pattern {0} not found at {1}'.format(
pattern, so_dict['sym_src_dir']
)
raise InstallError(message)
sym_dst_dir = os.path.abspath('../{0}'.format(
so_dict['sym_dst_dir']))
if not os.path.isdir(sym_dst_dir):
Cmd.mkdir_p(sym_dst_dir)
cmd = 'ln -sf {0} {1}/lib{2}.so'.format(so_files[0],
sym_dst_dir,
name)
Cmd.sh_e(cmd) | [
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6,776 | junaruga/rpm-py-installer | install.py | Installer._copy_each_include_files_to_include_dir | def _copy_each_include_files_to_include_dir(self):
"""Copy include header files for each directory to include directory.
Copy include header files
from
rpm/
rpmio/*.h
lib/*.h
build/*.h
sign/*.h
to
rpm/
include/
rpm/*.h
.
This is a status after running "make" on actual rpm build process.
"""
src_header_dirs = [
'rpmio',
'lib',
'build',
'sign',
]
with Cmd.pushd('..'):
src_include_dir = os.path.abspath('./include')
for header_dir in src_header_dirs:
if not os.path.isdir(header_dir):
message_format = "Skip not existing header directory '{0}'"
Log.debug(message_format.format(header_dir))
continue
header_files = Cmd.find(header_dir, '*.h')
for header_file in header_files:
pattern = '^{0}/'.format(header_dir)
(dst_header_file, subs_num) = re.subn(pattern,
'', header_file)
if subs_num == 0:
message = 'Failed to replace header_file: {0}'.format(
header_file)
raise ValueError(message)
dst_header_file = os.path.abspath(
os.path.join(src_include_dir, 'rpm', dst_header_file)
)
dst_dir = os.path.dirname(dst_header_file)
if not os.path.isdir(dst_dir):
Cmd.mkdir_p(dst_dir)
shutil.copyfile(header_file, dst_header_file) | python | def _copy_each_include_files_to_include_dir(self):
src_header_dirs = [
'rpmio',
'lib',
'build',
'sign',
]
with Cmd.pushd('..'):
src_include_dir = os.path.abspath('./include')
for header_dir in src_header_dirs:
if not os.path.isdir(header_dir):
message_format = "Skip not existing header directory '{0}'"
Log.debug(message_format.format(header_dir))
continue
header_files = Cmd.find(header_dir, '*.h')
for header_file in header_files:
pattern = '^{0}/'.format(header_dir)
(dst_header_file, subs_num) = re.subn(pattern,
'', header_file)
if subs_num == 0:
message = 'Failed to replace header_file: {0}'.format(
header_file)
raise ValueError(message)
dst_header_file = os.path.abspath(
os.path.join(src_include_dir, 'rpm', dst_header_file)
)
dst_dir = os.path.dirname(dst_header_file)
if not os.path.isdir(dst_dir):
Cmd.mkdir_p(dst_dir)
shutil.copyfile(header_file, dst_header_file) | [
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6,777 | junaruga/rpm-py-installer | install.py | Installer._rpm_py_has_popt_devel_dep | def _rpm_py_has_popt_devel_dep(self):
"""Check if the RPM Python binding has a depndency to popt-devel.
Search include header files in the source code to check it.
"""
found = False
with open('../include/rpm/rpmlib.h') as f_in:
for line in f_in:
if re.match(r'^#include .*popt.h.*$', line):
found = True
break
return found | python | def _rpm_py_has_popt_devel_dep(self):
found = False
with open('../include/rpm/rpmlib.h') as f_in:
for line in f_in:
if re.match(r'^#include .*popt.h.*$', line):
found = True
break
return found | [
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6,778 | junaruga/rpm-py-installer | install.py | FedoraInstaller.install_from_rpm_py_package | def install_from_rpm_py_package(self):
"""Run install from RPM Python binding RPM package."""
self._download_and_extract_rpm_py_package()
# Find ./usr/lib64/pythonN.N/site-packages/rpm directory.
# A binary built by same version Python with used Python is target
# for the safe installation.
if self.rpm.has_set_up_py_in():
# If RPM has setup.py.in, this strict check is okay.
# Because we can still install from the source.
py_dir_name = 'python{0}.{1}'.format(
sys.version_info[0], sys.version_info[1])
else:
# If RPM does not have setup.py.in such as CentOS6,
# Only way to install is by different Python's RPM package.
py_dir_name = '*'
python_lib_dir_pattern = os.path.join(
'usr', '*', py_dir_name, 'site-packages')
rpm_dir_pattern = os.path.join(python_lib_dir_pattern, 'rpm')
downloaded_rpm_dirs = glob.glob(rpm_dir_pattern)
if not downloaded_rpm_dirs:
message = 'Directory with a pattern: {0} not found.'.format(
rpm_dir_pattern)
raise RpmPyPackageNotFoundError(message)
src_rpm_dir = downloaded_rpm_dirs[0]
# Remove rpm directory for the possible installed directories.
for rpm_dir in self.python.python_lib_rpm_dirs:
if os.path.isdir(rpm_dir):
Log.debug("Remove existing rpm directory {0}".format(rpm_dir))
shutil.rmtree(rpm_dir)
dst_rpm_dir = self.python.python_lib_rpm_dir
Log.debug("Copy directory from '{0}' to '{1}'".format(
src_rpm_dir, dst_rpm_dir))
shutil.copytree(src_rpm_dir, dst_rpm_dir)
file_name_pattern = 'rpm-*.egg-info'
rpm_egg_info_pattern = os.path.join(
python_lib_dir_pattern, file_name_pattern)
downloaded_rpm_egg_infos = glob.glob(rpm_egg_info_pattern)
if downloaded_rpm_egg_infos:
existing_rpm_egg_info_pattern = os.path.join(
self.python.python_lib_dir, file_name_pattern)
existing_rpm_egg_infos = glob.glob(existing_rpm_egg_info_pattern)
for existing_rpm_egg_info in existing_rpm_egg_infos:
Log.debug("Remove existing rpm egg info file '{0}'".format(
existing_rpm_egg_info))
os.remove(existing_rpm_egg_info)
Log.debug("Copy file from '{0}' to '{1}'".format(
downloaded_rpm_egg_infos[0], self.python.python_lib_dir))
shutil.copy2(downloaded_rpm_egg_infos[0],
self.python.python_lib_dir) | python | def install_from_rpm_py_package(self):
self._download_and_extract_rpm_py_package()
# Find ./usr/lib64/pythonN.N/site-packages/rpm directory.
# A binary built by same version Python with used Python is target
# for the safe installation.
if self.rpm.has_set_up_py_in():
# If RPM has setup.py.in, this strict check is okay.
# Because we can still install from the source.
py_dir_name = 'python{0}.{1}'.format(
sys.version_info[0], sys.version_info[1])
else:
# If RPM does not have setup.py.in such as CentOS6,
# Only way to install is by different Python's RPM package.
py_dir_name = '*'
python_lib_dir_pattern = os.path.join(
'usr', '*', py_dir_name, 'site-packages')
rpm_dir_pattern = os.path.join(python_lib_dir_pattern, 'rpm')
downloaded_rpm_dirs = glob.glob(rpm_dir_pattern)
if not downloaded_rpm_dirs:
message = 'Directory with a pattern: {0} not found.'.format(
rpm_dir_pattern)
raise RpmPyPackageNotFoundError(message)
src_rpm_dir = downloaded_rpm_dirs[0]
# Remove rpm directory for the possible installed directories.
for rpm_dir in self.python.python_lib_rpm_dirs:
if os.path.isdir(rpm_dir):
Log.debug("Remove existing rpm directory {0}".format(rpm_dir))
shutil.rmtree(rpm_dir)
dst_rpm_dir = self.python.python_lib_rpm_dir
Log.debug("Copy directory from '{0}' to '{1}'".format(
src_rpm_dir, dst_rpm_dir))
shutil.copytree(src_rpm_dir, dst_rpm_dir)
file_name_pattern = 'rpm-*.egg-info'
rpm_egg_info_pattern = os.path.join(
python_lib_dir_pattern, file_name_pattern)
downloaded_rpm_egg_infos = glob.glob(rpm_egg_info_pattern)
if downloaded_rpm_egg_infos:
existing_rpm_egg_info_pattern = os.path.join(
self.python.python_lib_dir, file_name_pattern)
existing_rpm_egg_infos = glob.glob(existing_rpm_egg_info_pattern)
for existing_rpm_egg_info in existing_rpm_egg_infos:
Log.debug("Remove existing rpm egg info file '{0}'".format(
existing_rpm_egg_info))
os.remove(existing_rpm_egg_info)
Log.debug("Copy file from '{0}' to '{1}'".format(
downloaded_rpm_egg_infos[0], self.python.python_lib_dir))
shutil.copy2(downloaded_rpm_egg_infos[0],
self.python.python_lib_dir) | [
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6,779 | junaruga/rpm-py-installer | install.py | Linux.get_instance | def get_instance(cls, python, rpm_path, **kwargs):
"""Get OS object."""
linux = None
if Cmd.which('apt-get'):
linux = DebianLinux(python, rpm_path, **kwargs)
else:
linux = FedoraLinux(python, rpm_path, **kwargs)
return linux | python | def get_instance(cls, python, rpm_path, **kwargs):
linux = None
if Cmd.which('apt-get'):
linux = DebianLinux(python, rpm_path, **kwargs)
else:
linux = FedoraLinux(python, rpm_path, **kwargs)
return linux | [
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6,780 | junaruga/rpm-py-installer | install.py | Python.python_lib_rpm_dirs | def python_lib_rpm_dirs(self):
"""Both arch and non-arch site-packages directories."""
libs = [self.python_lib_arch_dir, self.python_lib_non_arch_dir]
def append_rpm(path):
return os.path.join(path, 'rpm')
return map(append_rpm, libs) | python | def python_lib_rpm_dirs(self):
libs = [self.python_lib_arch_dir, self.python_lib_non_arch_dir]
def append_rpm(path):
return os.path.join(path, 'rpm')
return map(append_rpm, libs) | [
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6,781 | junaruga/rpm-py-installer | install.py | Rpm.version | def version(self):
"""RPM vesion string."""
stdout = Cmd.sh_e_out('{0} --version'.format(self.rpm_path))
rpm_version = stdout.split()[2]
return rpm_version | python | def version(self):
stdout = Cmd.sh_e_out('{0} --version'.format(self.rpm_path))
rpm_version = stdout.split()[2]
return rpm_version | [
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6,782 | junaruga/rpm-py-installer | install.py | Rpm.is_system_rpm | def is_system_rpm(self):
"""Check if the RPM is system RPM."""
sys_rpm_paths = [
'/usr/bin/rpm',
# On CentOS6, system RPM is installed in this directory.
'/bin/rpm',
]
matched = False
for sys_rpm_path in sys_rpm_paths:
if self.rpm_path.startswith(sys_rpm_path):
matched = True
break
return matched | python | def is_system_rpm(self):
sys_rpm_paths = [
'/usr/bin/rpm',
# On CentOS6, system RPM is installed in this directory.
'/bin/rpm',
]
matched = False
for sys_rpm_path in sys_rpm_paths:
if self.rpm_path.startswith(sys_rpm_path):
matched = True
break
return matched | [
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6,783 | junaruga/rpm-py-installer | install.py | Rpm.is_package_installed | def is_package_installed(self, package_name):
"""Check if the RPM package is installed."""
if not package_name:
raise ValueError('package_name required.')
installed = True
try:
Cmd.sh_e('{0} --query {1} --quiet'.format(self.rpm_path,
package_name))
except InstallError:
installed = False
return installed | python | def is_package_installed(self, package_name):
if not package_name:
raise ValueError('package_name required.')
installed = True
try:
Cmd.sh_e('{0} --query {1} --quiet'.format(self.rpm_path,
package_name))
except InstallError:
installed = False
return installed | [
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6,784 | junaruga/rpm-py-installer | install.py | FedoraRpm.is_downloadable | def is_downloadable(self):
"""Return if rpm is downloadable by the package command.
Check if dnf or yum plugin package exists.
"""
is_plugin_avaiable = False
if self.is_dnf:
is_plugin_avaiable = self.is_package_installed(
'dnf-plugins-core')
else:
""" yum environment.
Make sure
# yum -y --downloadonly --downloaddir=. install package_name
is only available for root user.
yumdownloader in yum-utils is available for normal user.
https://access.redhat.com/solutions/10154
"""
is_plugin_avaiable = self.is_package_installed(
'yum-utils')
return is_plugin_avaiable | python | def is_downloadable(self):
is_plugin_avaiable = False
if self.is_dnf:
is_plugin_avaiable = self.is_package_installed(
'dnf-plugins-core')
else:
""" yum environment.
Make sure
# yum -y --downloadonly --downloaddir=. install package_name
is only available for root user.
yumdownloader in yum-utils is available for normal user.
https://access.redhat.com/solutions/10154
"""
is_plugin_avaiable = self.is_package_installed(
'yum-utils')
return is_plugin_avaiable | [
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6,785 | junaruga/rpm-py-installer | install.py | FedoraRpm.download | def download(self, package_name):
"""Download given package."""
if not package_name:
ValueError('package_name required.')
if self.is_dnf:
cmd = 'dnf download {0}.{1}'.format(package_name, self.arch)
else:
cmd = 'yumdownloader {0}.{1}'.format(package_name, self.arch)
try:
Cmd.sh_e(cmd, stdout=subprocess.PIPE)
except CmdError as e:
for out in (e.stdout, e.stderr):
for line in out.split('\n'):
if re.match(r'^No package [^ ]+ available', line) or \
re.match(r'^No Match for argument', line):
raise RemoteFileNotFoundError(
'Package {0} not found on remote'.format(
package_name
)
)
raise e | python | def download(self, package_name):
if not package_name:
ValueError('package_name required.')
if self.is_dnf:
cmd = 'dnf download {0}.{1}'.format(package_name, self.arch)
else:
cmd = 'yumdownloader {0}.{1}'.format(package_name, self.arch)
try:
Cmd.sh_e(cmd, stdout=subprocess.PIPE)
except CmdError as e:
for out in (e.stdout, e.stderr):
for line in out.split('\n'):
if re.match(r'^No package [^ ]+ available', line) or \
re.match(r'^No Match for argument', line):
raise RemoteFileNotFoundError(
'Package {0} not found on remote'.format(
package_name
)
)
raise e | [
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6,786 | junaruga/rpm-py-installer | install.py | FedoraRpm.extract | def extract(self, package_name):
"""Extract given package."""
for cmd in ['rpm2cpio', 'cpio']:
if not Cmd.which(cmd):
message = '{0} command not found. Install {0}.'.format(cmd)
raise InstallError(message)
pattern = '{0}*{1}.rpm'.format(package_name, self.arch)
rpm_files = Cmd.find('.', pattern)
if not rpm_files:
raise InstallError('PRM file not found.')
cmd = 'rpm2cpio {0} | cpio -idmv'.format(rpm_files[0])
Cmd.sh_e(cmd) | python | def extract(self, package_name):
for cmd in ['rpm2cpio', 'cpio']:
if not Cmd.which(cmd):
message = '{0} command not found. Install {0}.'.format(cmd)
raise InstallError(message)
pattern = '{0}*{1}.rpm'.format(package_name, self.arch)
rpm_files = Cmd.find('.', pattern)
if not rpm_files:
raise InstallError('PRM file not found.')
cmd = 'rpm2cpio {0} | cpio -idmv'.format(rpm_files[0])
Cmd.sh_e(cmd) | [
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6,787 | junaruga/rpm-py-installer | install.py | Cmd.sh_e | def sh_e(cls, cmd, **kwargs):
"""Run the command. It behaves like "sh -e".
It raises InstallError if the command failed.
"""
Log.debug('CMD: {0}'.format(cmd))
cmd_kwargs = {
'shell': True,
}
cmd_kwargs.update(kwargs)
env = os.environ.copy()
# Better to parse English output
env['LC_ALL'] = 'en_US.utf-8'
if 'env' in kwargs:
env.update(kwargs['env'])
cmd_kwargs['env'] = env
# Capture stderr to show it on error message.
cmd_kwargs['stderr'] = subprocess.PIPE
proc = None
try:
proc = subprocess.Popen(cmd, **cmd_kwargs)
stdout, stderr = proc.communicate()
returncode = proc.returncode
message_format = (
'CMD Return Code: [{0}], Stdout: [{1}], Stderr: [{2}]'
)
Log.debug(message_format.format(returncode, stdout, stderr))
if stdout is not None:
stdout = stdout.decode('utf-8')
if stderr is not None:
stderr = stderr.decode('utf-8')
if returncode != 0:
message = 'CMD: [{0}], Return Code: [{1}] at [{2}]'.format(
cmd, returncode, os.getcwd())
if stderr is not None:
message += ' Stderr: [{0}]'.format(stderr)
ie = CmdError(message)
ie.stdout = stdout
ie.stderr = stderr
raise ie
return (stdout, stderr)
except Exception as e:
try:
proc.kill()
except Exception:
pass
raise e | python | def sh_e(cls, cmd, **kwargs):
Log.debug('CMD: {0}'.format(cmd))
cmd_kwargs = {
'shell': True,
}
cmd_kwargs.update(kwargs)
env = os.environ.copy()
# Better to parse English output
env['LC_ALL'] = 'en_US.utf-8'
if 'env' in kwargs:
env.update(kwargs['env'])
cmd_kwargs['env'] = env
# Capture stderr to show it on error message.
cmd_kwargs['stderr'] = subprocess.PIPE
proc = None
try:
proc = subprocess.Popen(cmd, **cmd_kwargs)
stdout, stderr = proc.communicate()
returncode = proc.returncode
message_format = (
'CMD Return Code: [{0}], Stdout: [{1}], Stderr: [{2}]'
)
Log.debug(message_format.format(returncode, stdout, stderr))
if stdout is not None:
stdout = stdout.decode('utf-8')
if stderr is not None:
stderr = stderr.decode('utf-8')
if returncode != 0:
message = 'CMD: [{0}], Return Code: [{1}] at [{2}]'.format(
cmd, returncode, os.getcwd())
if stderr is not None:
message += ' Stderr: [{0}]'.format(stderr)
ie = CmdError(message)
ie.stdout = stdout
ie.stderr = stderr
raise ie
return (stdout, stderr)
except Exception as e:
try:
proc.kill()
except Exception:
pass
raise e | [
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6,788 | junaruga/rpm-py-installer | install.py | Cmd.sh_e_out | def sh_e_out(cls, cmd, **kwargs):
"""Run the command. and returns the stdout."""
cmd_kwargs = {
'stdout': subprocess.PIPE,
}
cmd_kwargs.update(kwargs)
return cls.sh_e(cmd, **cmd_kwargs)[0] | python | def sh_e_out(cls, cmd, **kwargs):
cmd_kwargs = {
'stdout': subprocess.PIPE,
}
cmd_kwargs.update(kwargs)
return cls.sh_e(cmd, **cmd_kwargs)[0] | [
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6,789 | junaruga/rpm-py-installer | install.py | Cmd.cd | def cd(cls, directory):
"""Change directory. It behaves like "cd directory"."""
Log.debug('CMD: cd {0}'.format(directory))
os.chdir(directory) | python | def cd(cls, directory):
Log.debug('CMD: cd {0}'.format(directory))
os.chdir(directory) | [
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6,790 | junaruga/rpm-py-installer | install.py | Cmd.pushd | def pushd(cls, new_dir):
"""Change directory, and back to previous directory.
It behaves like "pushd directory; something; popd".
"""
previous_dir = os.getcwd()
try:
new_ab_dir = None
if os.path.isabs(new_dir):
new_ab_dir = new_dir
else:
new_ab_dir = os.path.join(previous_dir, new_dir)
# Use absolute path to show it on FileNotFoundError message.
cls.cd(new_ab_dir)
yield
finally:
cls.cd(previous_dir) | python | def pushd(cls, new_dir):
previous_dir = os.getcwd()
try:
new_ab_dir = None
if os.path.isabs(new_dir):
new_ab_dir = new_dir
else:
new_ab_dir = os.path.join(previous_dir, new_dir)
# Use absolute path to show it on FileNotFoundError message.
cls.cd(new_ab_dir)
yield
finally:
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6,791 | junaruga/rpm-py-installer | install.py | Cmd.which | def which(cls, cmd):
"""Return an absolute path of the command.
It behaves like "which command".
"""
abs_path_cmd = None
if sys.version_info >= (3, 3):
abs_path_cmd = shutil.which(cmd)
else:
abs_path_cmd = find_executable(cmd)
return abs_path_cmd | python | def which(cls, cmd):
abs_path_cmd = None
if sys.version_info >= (3, 3):
abs_path_cmd = shutil.which(cmd)
else:
abs_path_cmd = find_executable(cmd)
return abs_path_cmd | [
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6,792 | junaruga/rpm-py-installer | install.py | Cmd.curl_remote_name | def curl_remote_name(cls, file_url):
"""Download file_url, and save as a file name of the URL.
It behaves like "curl -O or --remote-name".
It raises HTTPError if the file_url not found.
"""
tar_gz_file_name = file_url.split('/')[-1]
if sys.version_info >= (3, 2):
from urllib.request import urlopen
from urllib.error import HTTPError
else:
from urllib2 import urlopen
from urllib2 import HTTPError
response = None
try:
response = urlopen(file_url)
except HTTPError as e:
message = 'Download failed: URL: {0}, reason: {1}'.format(
file_url, e)
if 'HTTP Error 404' in str(e):
raise RemoteFileNotFoundError(message)
else:
raise InstallError(message)
tar_gz_file_obj = io.BytesIO(response.read())
with open(tar_gz_file_name, 'wb') as f_out:
f_out.write(tar_gz_file_obj.read())
return tar_gz_file_name | python | def curl_remote_name(cls, file_url):
tar_gz_file_name = file_url.split('/')[-1]
if sys.version_info >= (3, 2):
from urllib.request import urlopen
from urllib.error import HTTPError
else:
from urllib2 import urlopen
from urllib2 import HTTPError
response = None
try:
response = urlopen(file_url)
except HTTPError as e:
message = 'Download failed: URL: {0}, reason: {1}'.format(
file_url, e)
if 'HTTP Error 404' in str(e):
raise RemoteFileNotFoundError(message)
else:
raise InstallError(message)
tar_gz_file_obj = io.BytesIO(response.read())
with open(tar_gz_file_name, 'wb') as f_out:
f_out.write(tar_gz_file_obj.read())
return tar_gz_file_name | [
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6,793 | junaruga/rpm-py-installer | install.py | Cmd.tar_extract | def tar_extract(cls, tar_comp_file_path):
"""Extract tar.gz or tar bz2 file.
It behaves like
- tar xzf tar_gz_file_path
- tar xjf tar_bz2_file_path
It raises tarfile.ReadError if the file is broken.
"""
try:
with contextlib.closing(tarfile.open(tar_comp_file_path)) as tar:
tar.extractall()
except tarfile.ReadError as e:
message_format = (
'Extract failed: '
'tar_comp_file_path: {0}, reason: {1}'
)
raise InstallError(message_format.format(tar_comp_file_path, e)) | python | def tar_extract(cls, tar_comp_file_path):
try:
with contextlib.closing(tarfile.open(tar_comp_file_path)) as tar:
tar.extractall()
except tarfile.ReadError as e:
message_format = (
'Extract failed: '
'tar_comp_file_path: {0}, reason: {1}'
)
raise InstallError(message_format.format(tar_comp_file_path, e)) | [
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6,794 | junaruga/rpm-py-installer | install.py | Cmd.find | def find(cls, searched_dir, pattern):
"""Find matched files.
It does not include symbolic file in the result.
"""
Log.debug('find {0} with pattern: {1}'.format(searched_dir, pattern))
matched_files = []
for root_dir, dir_names, file_names in os.walk(searched_dir,
followlinks=False):
for file_name in file_names:
if fnmatch.fnmatch(file_name, pattern):
file_path = os.path.join(root_dir, file_name)
if not os.path.islink(file_path):
matched_files.append(file_path)
matched_files.sort()
return matched_files | python | def find(cls, searched_dir, pattern):
Log.debug('find {0} with pattern: {1}'.format(searched_dir, pattern))
matched_files = []
for root_dir, dir_names, file_names in os.walk(searched_dir,
followlinks=False):
for file_name in file_names:
if fnmatch.fnmatch(file_name, pattern):
file_path = os.path.join(root_dir, file_name)
if not os.path.islink(file_path):
matched_files.append(file_path)
matched_files.sort()
return matched_files | [
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6,795 | junaruga/rpm-py-installer | install.py | Utils.version_str2tuple | def version_str2tuple(cls, version_str):
"""Version info.
tuple object. ex. ('4', '14', '0', 'rc1')
"""
if not isinstance(version_str, str):
ValueError('version_str invalid instance.')
version_info_list = re.findall(r'[0-9a-zA-Z]+', version_str)
def convert_to_int(string):
value = None
if re.match(r'^\d+$', string):
value = int(string)
else:
value = string
return value
version_info_list = [convert_to_int(s) for s in version_info_list]
return tuple(version_info_list) | python | def version_str2tuple(cls, version_str):
if not isinstance(version_str, str):
ValueError('version_str invalid instance.')
version_info_list = re.findall(r'[0-9a-zA-Z]+', version_str)
def convert_to_int(string):
value = None
if re.match(r'^\d+$', string):
value = int(string)
else:
value = string
return value
version_info_list = [convert_to_int(s) for s in version_info_list]
return tuple(version_info_list) | [
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6,796 | junaruga/rpm-py-installer | setup.py | install_rpm_py | def install_rpm_py():
"""Install RPM Python binding."""
python_path = sys.executable
cmd = '{0} install.py'.format(python_path)
exit_status = os.system(cmd)
if exit_status != 0:
raise Exception('Command failed: {0}'.format(cmd)) | python | def install_rpm_py():
python_path = sys.executable
cmd = '{0} install.py'.format(python_path)
exit_status = os.system(cmd)
if exit_status != 0:
raise Exception('Command failed: {0}'.format(cmd)) | [
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6,797 | biocommons/biocommons.seqrepo | biocommons/seqrepo/fastadir/fabgz.py | _get_bgzip_version | def _get_bgzip_version(exe):
"""return bgzip version as string"""
p = subprocess.Popen([exe, "-h"], stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True)
output = p.communicate()
version_line = output[0].splitlines()[1]
version = re.match(r"(?:Version:|bgzip \(htslib\))\s+(\d+\.\d+(\.\d+)?)", version_line).group(1)
return version | python | def _get_bgzip_version(exe):
p = subprocess.Popen([exe, "-h"], stdout=subprocess.PIPE, stderr=subprocess.STDOUT, universal_newlines=True)
output = p.communicate()
version_line = output[0].splitlines()[1]
version = re.match(r"(?:Version:|bgzip \(htslib\))\s+(\d+\.\d+(\.\d+)?)", version_line).group(1)
return version | [
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6,798 | biocommons/biocommons.seqrepo | biocommons/seqrepo/fastadir/fabgz.py | _find_bgzip | def _find_bgzip():
"""return path to bgzip if found and meets version requirements, else exception"""
missing_file_exception = OSError if six.PY2 else FileNotFoundError
min_bgzip_version = ".".join(map(str, min_bgzip_version_info))
exe = os.environ.get("SEQREPO_BGZIP_PATH", which("bgzip") or "/usr/bin/bgzip")
try:
bgzip_version = _get_bgzip_version(exe)
except AttributeError:
raise RuntimeError("Didn't find version string in bgzip executable ({exe})".format(exe=exe))
except missing_file_exception:
raise RuntimeError("{exe} doesn't exist; you need to install htslib (See https://github.com/biocommons/biocommons.seqrepo#requirements)".format(exe=exe))
except Exception:
raise RuntimeError("Unknown error while executing {exe}".format(exe=exe))
bgzip_version_info = tuple(map(int, bgzip_version.split(".")))
if bgzip_version_info < min_bgzip_version_info:
raise RuntimeError("bgzip ({exe}) {ev} is too old; >= {rv} is required; please upgrade".format(
exe=exe, ev=bgzip_version, rv=min_bgzip_version))
logger.info("Using bgzip {ev} ({exe})".format(ev=bgzip_version, exe=exe))
return exe | python | def _find_bgzip():
missing_file_exception = OSError if six.PY2 else FileNotFoundError
min_bgzip_version = ".".join(map(str, min_bgzip_version_info))
exe = os.environ.get("SEQREPO_BGZIP_PATH", which("bgzip") or "/usr/bin/bgzip")
try:
bgzip_version = _get_bgzip_version(exe)
except AttributeError:
raise RuntimeError("Didn't find version string in bgzip executable ({exe})".format(exe=exe))
except missing_file_exception:
raise RuntimeError("{exe} doesn't exist; you need to install htslib (See https://github.com/biocommons/biocommons.seqrepo#requirements)".format(exe=exe))
except Exception:
raise RuntimeError("Unknown error while executing {exe}".format(exe=exe))
bgzip_version_info = tuple(map(int, bgzip_version.split(".")))
if bgzip_version_info < min_bgzip_version_info:
raise RuntimeError("bgzip ({exe}) {ev} is too old; >= {rv} is required; please upgrade".format(
exe=exe, ev=bgzip_version, rv=min_bgzip_version))
logger.info("Using bgzip {ev} ({exe})".format(ev=bgzip_version, exe=exe))
return exe | [
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6,799 | biocommons/biocommons.seqrepo | biocommons/seqrepo/seqrepo.py | SeqRepo.translate_alias | def translate_alias(self, alias, namespace=None, target_namespaces=None, translate_ncbi_namespace=None):
"""given an alias and optional namespace, return a list of all other
aliases for same sequence
"""
if translate_ncbi_namespace is None:
translate_ncbi_namespace = self.translate_ncbi_namespace
seq_id = self._get_unique_seqid(alias=alias, namespace=namespace)
aliases = self.aliases.fetch_aliases(seq_id=seq_id,
translate_ncbi_namespace=translate_ncbi_namespace)
if target_namespaces:
aliases = [a for a in aliases if a["namespace"] in target_namespaces]
return aliases | python | def translate_alias(self, alias, namespace=None, target_namespaces=None, translate_ncbi_namespace=None):
if translate_ncbi_namespace is None:
translate_ncbi_namespace = self.translate_ncbi_namespace
seq_id = self._get_unique_seqid(alias=alias, namespace=namespace)
aliases = self.aliases.fetch_aliases(seq_id=seq_id,
translate_ncbi_namespace=translate_ncbi_namespace)
if target_namespaces:
aliases = [a for a in aliases if a["namespace"] in target_namespaces]
return aliases | [
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"same",
"sequence"
] | fb6d88682cb73ee6971cfa47d4dcd90a9c649167 | https://github.com/biocommons/biocommons.seqrepo/blob/fb6d88682cb73ee6971cfa47d4dcd90a9c649167/biocommons/seqrepo/seqrepo.py#L175-L188 |
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