repository_name stringlengths 5 67 | func_path_in_repository stringlengths 4 234 | func_name stringlengths 0 314 | whole_func_string stringlengths 52 3.87M | language stringclasses 6
values | func_code_string stringlengths 52 3.87M | func_documentation_string stringlengths 1 47.2k | func_code_url stringlengths 85 339 |
|---|---|---|---|---|---|---|---|
bslatkin/dpxdt | dpxdt/server/api.py | runs_done | def runs_done():
"""Marks a release candidate as having all runs reported."""
build = g.build
release_name, release_number = _get_release_params()
release = (
models.Release.query
.filter_by(build_id=build.id, name=release_name, number=release_number)
.with_lockmode('update')
... | python | def runs_done():
"""Marks a release candidate as having all runs reported."""
build = g.build
release_name, release_number = _get_release_params()
release = (
models.Release.query
.filter_by(build_id=build.id, name=release_name, number=release_number)
.with_lockmode('update')
... | Marks a release candidate as having all runs reported. | https://github.com/bslatkin/dpxdt/blob/9f860de1731021d99253670429e5f2157e1f6297/dpxdt/server/api.py#L531-L562 |
bslatkin/dpxdt | dpxdt/server/api.py | _save_artifact | def _save_artifact(build, data, content_type):
"""Saves an artifact to the DB and returns it."""
sha1sum = hashlib.sha1(data).hexdigest()
artifact = models.Artifact.query.filter_by(id=sha1sum).first()
if artifact:
logging.debug('Upload already exists: artifact_id=%r', sha1sum)
else:
log... | python | def _save_artifact(build, data, content_type):
"""Saves an artifact to the DB and returns it."""
sha1sum = hashlib.sha1(data).hexdigest()
artifact = models.Artifact.query.filter_by(id=sha1sum).first()
if artifact:
logging.debug('Upload already exists: artifact_id=%r', sha1sum)
else:
log... | Saves an artifact to the DB and returns it. | https://github.com/bslatkin/dpxdt/blob/9f860de1731021d99253670429e5f2157e1f6297/dpxdt/server/api.py#L575-L592 |
bslatkin/dpxdt | dpxdt/server/api.py | upload | def upload():
"""Uploads an artifact referenced by a run."""
build = g.build
utils.jsonify_assert(len(request.files) == 1,
'Need exactly one uploaded file')
file_storage = request.files.values()[0]
data = file_storage.read()
content_type, _ = mimetypes.guess_type(file_s... | python | def upload():
"""Uploads an artifact referenced by a run."""
build = g.build
utils.jsonify_assert(len(request.files) == 1,
'Need exactly one uploaded file')
file_storage = request.files.values()[0]
data = file_storage.read()
content_type, _ = mimetypes.guess_type(file_s... | Uploads an artifact referenced by a run. | https://github.com/bslatkin/dpxdt/blob/9f860de1731021d99253670429e5f2157e1f6297/dpxdt/server/api.py#L598-L617 |
bslatkin/dpxdt | dpxdt/server/api.py | _get_artifact_response | def _get_artifact_response(artifact):
"""Gets the response object for the given artifact.
This method may be overridden in environments that have a different way of
storing artifact files, such as on-disk or S3.
"""
response = flask.Response(
artifact.data,
mimetype=artifact.content... | python | def _get_artifact_response(artifact):
"""Gets the response object for the given artifact.
This method may be overridden in environments that have a different way of
storing artifact files, such as on-disk or S3.
"""
response = flask.Response(
artifact.data,
mimetype=artifact.content... | Gets the response object for the given artifact.
This method may be overridden in environments that have a different way of
storing artifact files, such as on-disk or S3. | https://github.com/bslatkin/dpxdt/blob/9f860de1731021d99253670429e5f2157e1f6297/dpxdt/server/api.py#L620-L632 |
bslatkin/dpxdt | dpxdt/server/api.py | download | def download():
"""Downloads an artifact by it's content hash."""
# Allow users with access to the build to download the file. Falls back
# to API keys with access to the build. Prefer user first for speed.
try:
build = auth.can_user_access_build('build_id')
except HTTPException:
log... | python | def download():
"""Downloads an artifact by it's content hash."""
# Allow users with access to the build to download the file. Falls back
# to API keys with access to the build. Prefer user first for speed.
try:
build = auth.can_user_access_build('build_id')
except HTTPException:
log... | Downloads an artifact by it's content hash. | https://github.com/bslatkin/dpxdt/blob/9f860de1731021d99253670429e5f2157e1f6297/dpxdt/server/api.py#L636-L682 |
bslatkin/dpxdt | dpxdt/client/pdiff_worker.py | register | def register(coordinator):
"""Registers this module as a worker with the given coordinator."""
utils.verify_binary('pdiff_compare_binary', ['-version'])
utils.verify_binary('pdiff_composite_binary', ['-version'])
assert FLAGS.pdiff_threads > 0
assert FLAGS.queue_server_prefix
item = queue_work... | python | def register(coordinator):
"""Registers this module as a worker with the given coordinator."""
utils.verify_binary('pdiff_compare_binary', ['-version'])
utils.verify_binary('pdiff_composite_binary', ['-version'])
assert FLAGS.pdiff_threads > 0
assert FLAGS.queue_server_prefix
item = queue_work... | Registers this module as a worker with the given coordinator. | https://github.com/bslatkin/dpxdt/blob/9f860de1731021d99253670429e5f2157e1f6297/dpxdt/client/pdiff_worker.py#L226-L240 |
bslatkin/dpxdt | dpxdt/server/operations.py | BaseOps.evict | def evict(self):
"""Evict all caches related to these operations."""
logging.debug('Evicting cache for %r', self.cache_key)
_clear_version_cache(self.cache_key)
# Cause the cache key to be refreshed next time any operation is
# run to make sure we don't act on old cached data.
... | python | def evict(self):
"""Evict all caches related to these operations."""
logging.debug('Evicting cache for %r', self.cache_key)
_clear_version_cache(self.cache_key)
# Cause the cache key to be refreshed next time any operation is
# run to make sure we don't act on old cached data.
... | Evict all caches related to these operations. | https://github.com/bslatkin/dpxdt/blob/9f860de1731021d99253670429e5f2157e1f6297/dpxdt/server/operations.py#L72-L78 |
bslatkin/dpxdt | dpxdt/server/operations.py | BuildOps.sort_run | def sort_run(run):
"""Sort function for runs within a release."""
# Sort errors first, then by name. Also show errors that were manually
# approved, so the paging sort order stays the same even after users
# approve a diff on the run page.
if run.status in models.Run.DIFF_NEEDED_... | python | def sort_run(run):
"""Sort function for runs within a release."""
# Sort errors first, then by name. Also show errors that were manually
# approved, so the paging sort order stays the same even after users
# approve a diff on the run page.
if run.status in models.Run.DIFF_NEEDED_... | Sort function for runs within a release. | https://github.com/bslatkin/dpxdt/blob/9f860de1731021d99253670429e5f2157e1f6297/dpxdt/server/operations.py#L170-L177 |
podio/valideer | valideer/base.py | parse | def parse(obj, required_properties=None, additional_properties=None,
ignore_optional_property_errors=None):
"""Try to parse the given ``obj`` as a validator instance.
:param obj: The object to be parsed. If it is a...:
- :py:class:`Validator` instance, return it.
- :py:class:`Validat... | python | def parse(obj, required_properties=None, additional_properties=None,
ignore_optional_property_errors=None):
"""Try to parse the given ``obj`` as a validator instance.
:param obj: The object to be parsed. If it is a...:
- :py:class:`Validator` instance, return it.
- :py:class:`Validat... | Try to parse the given ``obj`` as a validator instance.
:param obj: The object to be parsed. If it is a...:
- :py:class:`Validator` instance, return it.
- :py:class:`Validator` subclass, instantiate it without arguments and
return it.
- :py:attr:`~Validator.name` of a known :py:c... | https://github.com/podio/valideer/blob/d35be173cb40c9fa1adb879673786b346b6841db/valideer/base.py#L60-L165 |
podio/valideer | valideer/base.py | parsing | def parsing(**kwargs):
"""
Context manager for overriding the default validator parsing rules for the
following code block.
"""
from .validators import Object
with _VALIDATOR_FACTORIES_LOCK:
old_values = {}
for key, value in iteritems(kwargs):
if value is not None:
... | python | def parsing(**kwargs):
"""
Context manager for overriding the default validator parsing rules for the
following code block.
"""
from .validators import Object
with _VALIDATOR_FACTORIES_LOCK:
old_values = {}
for key, value in iteritems(kwargs):
if value is not None:
... | Context manager for overriding the default validator parsing rules for the
following code block. | https://github.com/podio/valideer/blob/d35be173cb40c9fa1adb879673786b346b6841db/valideer/base.py#L169-L188 |
podio/valideer | valideer/base.py | register | def register(name, validator):
"""Register a validator instance under the given ``name``."""
if not isinstance(validator, Validator):
raise TypeError("Validator instance expected, %s given" % validator.__class__)
_NAMED_VALIDATORS[name] = validator | python | def register(name, validator):
"""Register a validator instance under the given ``name``."""
if not isinstance(validator, Validator):
raise TypeError("Validator instance expected, %s given" % validator.__class__)
_NAMED_VALIDATORS[name] = validator | Register a validator instance under the given ``name``. | https://github.com/podio/valideer/blob/d35be173cb40c9fa1adb879673786b346b6841db/valideer/base.py#L191-L195 |
podio/valideer | valideer/base.py | accepts | def accepts(**schemas):
"""Create a decorator for validating function parameters.
Example::
@accepts(a="number", body={"+field_ids": [int], "is_ok": bool})
def f(a, body):
print (a, body["field_ids"], body.get("is_ok"))
:param schemas: The schema for validating a given paramet... | python | def accepts(**schemas):
"""Create a decorator for validating function parameters.
Example::
@accepts(a="number", body={"+field_ids": [int], "is_ok": bool})
def f(a, body):
print (a, body["field_ids"], body.get("is_ok"))
:param schemas: The schema for validating a given paramet... | Create a decorator for validating function parameters.
Example::
@accepts(a="number", body={"+field_ids": [int], "is_ok": bool})
def f(a, body):
print (a, body["field_ids"], body.get("is_ok"))
:param schemas: The schema for validating a given parameter. | https://github.com/podio/valideer/blob/d35be173cb40c9fa1adb879673786b346b6841db/valideer/base.py#L272-L289 |
podio/valideer | valideer/base.py | returns | def returns(schema):
"""Create a decorator for validating function return value.
Example::
@accepts(a=int, b=int)
@returns(int)
def f(a, b):
return a + b
:param schema: The schema for adapting a given parameter.
"""
validate = parse(schema).validate
@decora... | python | def returns(schema):
"""Create a decorator for validating function return value.
Example::
@accepts(a=int, b=int)
@returns(int)
def f(a, b):
return a + b
:param schema: The schema for adapting a given parameter.
"""
validate = parse(schema).validate
@decora... | Create a decorator for validating function return value.
Example::
@accepts(a=int, b=int)
@returns(int)
def f(a, b):
return a + b
:param schema: The schema for adapting a given parameter. | https://github.com/podio/valideer/blob/d35be173cb40c9fa1adb879673786b346b6841db/valideer/base.py#L292-L310 |
podio/valideer | valideer/base.py | adapts | def adapts(**schemas):
"""Create a decorator for validating and adapting function parameters.
Example::
@adapts(a="number", body={"+field_ids": [V.AdaptTo(int)], "is_ok": bool})
def f(a, body):
print (a, body.field_ids, body.is_ok)
:param schemas: The schema for adapting a giv... | python | def adapts(**schemas):
"""Create a decorator for validating and adapting function parameters.
Example::
@adapts(a="number", body={"+field_ids": [V.AdaptTo(int)], "is_ok": bool})
def f(a, body):
print (a, body.field_ids, body.is_ok)
:param schemas: The schema for adapting a giv... | Create a decorator for validating and adapting function parameters.
Example::
@adapts(a="number", body={"+field_ids": [V.AdaptTo(int)], "is_ok": bool})
def f(a, body):
print (a, body.field_ids, body.is_ok)
:param schemas: The schema for adapting a given parameter. | https://github.com/podio/valideer/blob/d35be173cb40c9fa1adb879673786b346b6841db/valideer/base.py#L313-L346 |
podio/valideer | valideer/validators.py | _ObjectFactory | def _ObjectFactory(obj):
"""Parse a python ``{name: schema}`` dict as an :py:class:`Object` instance.
- A property name prepended by "+" is required
- A property name prepended by "?" is optional
- Any other property is required if :py:attr:`Object.REQUIRED_PROPERTIES`
is True else it's optional
... | python | def _ObjectFactory(obj):
"""Parse a python ``{name: schema}`` dict as an :py:class:`Object` instance.
- A property name prepended by "+" is required
- A property name prepended by "?" is optional
- Any other property is required if :py:attr:`Object.REQUIRED_PROPERTIES`
is True else it's optional
... | Parse a python ``{name: schema}`` dict as an :py:class:`Object` instance.
- A property name prepended by "+" is required
- A property name prepended by "?" is optional
- Any other property is required if :py:attr:`Object.REQUIRED_PROPERTIES`
is True else it's optional | https://github.com/podio/valideer/blob/d35be173cb40c9fa1adb879673786b346b6841db/valideer/validators.py#L713-L732 |
HumanCellAtlas/dcp-cli | hca/upload/lib/client_side_checksum_handler.py | ClientSideChecksumHandler.get_checksum_metadata_tag | def get_checksum_metadata_tag(self):
""" Returns a map of checksum values by the name of the hashing function that produced it."""
if not self._checksums:
print("Warning: No checksums have been computed for this file.")
return {str(_hash_name): str(_hash_value) for _hash_name, _hash_... | python | def get_checksum_metadata_tag(self):
""" Returns a map of checksum values by the name of the hashing function that produced it."""
if not self._checksums:
print("Warning: No checksums have been computed for this file.")
return {str(_hash_name): str(_hash_value) for _hash_name, _hash_... | Returns a map of checksum values by the name of the hashing function that produced it. | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/lib/client_side_checksum_handler.py#L20-L24 |
HumanCellAtlas/dcp-cli | hca/upload/lib/client_side_checksum_handler.py | ClientSideChecksumHandler.compute_checksum | def compute_checksum(self):
""" Calculates checksums for a given file. """
if self._filename.startswith("s3://"):
print("Warning: Did not perform client-side checksumming for file in S3. To be implemented.")
pass
else:
checksumCalculator = self.ChecksumCalcula... | python | def compute_checksum(self):
""" Calculates checksums for a given file. """
if self._filename.startswith("s3://"):
print("Warning: Did not perform client-side checksumming for file in S3. To be implemented.")
pass
else:
checksumCalculator = self.ChecksumCalcula... | Calculates checksums for a given file. | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/lib/client_side_checksum_handler.py#L26-L33 |
HumanCellAtlas/dcp-cli | hca/upload/upload_area.py | UploadArea.get_credentials | def get_credentials(self):
"""
Return a set of credentials that may be used to access the Upload Area folder in the S3 bucket
:return: a dict containing AWS credentials in a format suitable for passing to Boto3
or if capitalized, used as environment variables
"""
cred... | python | def get_credentials(self):
"""
Return a set of credentials that may be used to access the Upload Area folder in the S3 bucket
:return: a dict containing AWS credentials in a format suitable for passing to Boto3
or if capitalized, used as environment variables
"""
cred... | Return a set of credentials that may be used to access the Upload Area folder in the S3 bucket
:return: a dict containing AWS credentials in a format suitable for passing to Boto3
or if capitalized, used as environment variables | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/upload_area.py#L57-L70 |
HumanCellAtlas/dcp-cli | hca/upload/upload_area.py | UploadArea.list | def list(self, detail=False):
"""
A generator that yields information about each file in the upload area
:param detail: return detailed file information (slower)
:return: a list of dicts containing at least 'name', or more of detail was requested
"""
creds_provider = Cred... | python | def list(self, detail=False):
"""
A generator that yields information about each file in the upload area
:param detail: return detailed file information (slower)
:return: a list of dicts containing at least 'name', or more of detail was requested
"""
creds_provider = Cred... | A generator that yields information about each file in the upload area
:param detail: return detailed file information (slower)
:return: a list of dicts containing at least 'name', or more of detail was requested | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/upload_area.py#L72-L89 |
HumanCellAtlas/dcp-cli | hca/upload/upload_area.py | UploadArea.store_file | def store_file(self, filename, file_content, content_type):
"""
Store a small file in an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param str filename: The name the file will have in the Upload Area
:param str file_content: The contents of the ... | python | def store_file(self, filename, file_content, content_type):
"""
Store a small file in an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param str filename: The name the file will have in the Upload Area
:param str file_content: The contents of the ... | Store a small file in an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param str filename: The name the file will have in the Upload Area
:param str file_content: The contents of the file
:param str content_type: The MIME-type for the file
:return... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/upload_area.py#L91-L107 |
HumanCellAtlas/dcp-cli | hca/upload/upload_area.py | UploadArea.upload_files | def upload_files(self, file_paths, file_size_sum=0, dcp_type="data", target_filename=None,
use_transfer_acceleration=True, report_progress=False, sync=True):
"""
A function that takes in a list of file paths and other optional args for parallel file upload
"""
self._... | python | def upload_files(self, file_paths, file_size_sum=0, dcp_type="data", target_filename=None,
use_transfer_acceleration=True, report_progress=False, sync=True):
"""
A function that takes in a list of file paths and other optional args for parallel file upload
"""
self._... | A function that takes in a list of file paths and other optional args for parallel file upload | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/upload_area.py#L109-L138 |
HumanCellAtlas/dcp-cli | hca/upload/upload_area.py | UploadArea.validate_files | def validate_files(self, file_list, validator_image, original_validation_id="", environment={}):
"""
Invoke supplied validator Docker image and give it access to the file/s.
The validator must be based off the base validator Docker image.
:param list file_list: A list of files within th... | python | def validate_files(self, file_list, validator_image, original_validation_id="", environment={}):
"""
Invoke supplied validator Docker image and give it access to the file/s.
The validator must be based off the base validator Docker image.
:param list file_list: A list of files within th... | Invoke supplied validator Docker image and give it access to the file/s.
The validator must be based off the base validator Docker image.
:param list file_list: A list of files within the Upload Area to be validated
:param str validator_image: the location of a docker image to use for validatio... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/upload_area.py#L140-L157 |
HumanCellAtlas/dcp-cli | hca/upload/upload_area.py | UploadArea.checksum_status | def checksum_status(self, filename):
"""
Retrieve checksum status and values for a file
:param str filename: The name of the file within the Upload Area
:return: a dict with checksum information
:rtype: dict
:raises UploadApiException: if information could not be obtaine... | python | def checksum_status(self, filename):
"""
Retrieve checksum status and values for a file
:param str filename: The name of the file within the Upload Area
:return: a dict with checksum information
:rtype: dict
:raises UploadApiException: if information could not be obtaine... | Retrieve checksum status and values for a file
:param str filename: The name of the file within the Upload Area
:return: a dict with checksum information
:rtype: dict
:raises UploadApiException: if information could not be obtained | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/upload_area.py#L159-L168 |
HumanCellAtlas/dcp-cli | hca/upload/upload_area.py | UploadArea.validation_status | def validation_status(self, filename):
"""
Get status and results of latest validation job for a file.
:param str filename: The name of the file within the Upload Area
:return: a dict with validation information
:rtype: dict
:raises UploadApiException: if information cou... | python | def validation_status(self, filename):
"""
Get status and results of latest validation job for a file.
:param str filename: The name of the file within the Upload Area
:return: a dict with validation information
:rtype: dict
:raises UploadApiException: if information cou... | Get status and results of latest validation job for a file.
:param str filename: The name of the file within the Upload Area
:return: a dict with validation information
:rtype: dict
:raises UploadApiException: if information could not be obtained | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/upload_area.py#L181-L190 |
HumanCellAtlas/dcp-cli | hca/cli.py | check_if_release_is_current | def check_if_release_is_current(log):
"""Warns the user if their release is behind the latest PyPi __version__."""
if __version__ == '0.0.0':
return
client = xmlrpclib.ServerProxy('https://pypi.python.org/pypi')
latest_pypi_version = client.package_releases('hca')
latest_version_nums = [int... | python | def check_if_release_is_current(log):
"""Warns the user if their release is behind the latest PyPi __version__."""
if __version__ == '0.0.0':
return
client = xmlrpclib.ServerProxy('https://pypi.python.org/pypi')
latest_pypi_version = client.package_releases('hca')
latest_version_nums = [int... | Warns the user if their release is behind the latest PyPi __version__. | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/cli.py#L61-L81 |
HumanCellAtlas/dcp-cli | hca/util/_docs.py | _parse_docstring | def _parse_docstring(docstring):
"""
Using the sphinx RSTParse to parse __doc__ for argparse `parameters`, `help`, and `description`. The first
rst paragraph encountered it treated as the argparse help text. Any param fields are treated as argparse
arguments. Any other text is combined and added to the ... | python | def _parse_docstring(docstring):
"""
Using the sphinx RSTParse to parse __doc__ for argparse `parameters`, `help`, and `description`. The first
rst paragraph encountered it treated as the argparse help text. Any param fields are treated as argparse
arguments. Any other text is combined and added to the ... | Using the sphinx RSTParse to parse __doc__ for argparse `parameters`, `help`, and `description`. The first
rst paragraph encountered it treated as the argparse help text. Any param fields are treated as argparse
arguments. Any other text is combined and added to the argparse description.
example:
\... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/util/_docs.py#L51-L98 |
HumanCellAtlas/dcp-cli | hca/upload/lib/s3_agent.py | sizeof_fmt | def sizeof_fmt(num, suffix='B'):
"""
Adapted from https://stackoverflow.com/a/1094933
Re: precision - display enough decimals to show progress on a slow (<5 MB/s) Internet connection
"""
precision = {'': 0, 'Ki': 0, 'Mi': 0, 'Gi': 3, 'Ti': 6, 'Pi': 9, 'Ei': 12, 'Zi': 15}
for unit in ['', 'Ki', ... | python | def sizeof_fmt(num, suffix='B'):
"""
Adapted from https://stackoverflow.com/a/1094933
Re: precision - display enough decimals to show progress on a slow (<5 MB/s) Internet connection
"""
precision = {'': 0, 'Ki': 0, 'Mi': 0, 'Gi': 3, 'Ti': 6, 'Pi': 9, 'Ei': 12, 'Zi': 15}
for unit in ['', 'Ki', ... | Adapted from https://stackoverflow.com/a/1094933
Re: precision - display enough decimals to show progress on a slow (<5 MB/s) Internet connection | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/lib/s3_agent.py#L16-L28 |
HumanCellAtlas/dcp-cli | hca/upload/lib/s3_agent.py | S3Agent._item_exists_in_bucket | def _item_exists_in_bucket(self, bucket, key, checksums):
""" Returns true if the key already exists in the current bucket and the clientside checksum matches the
file's checksums, and false otherwise."""
try:
obj = self.target_s3.meta.client.head_object(Bucket=bucket, Key=key)
... | python | def _item_exists_in_bucket(self, bucket, key, checksums):
""" Returns true if the key already exists in the current bucket and the clientside checksum matches the
file's checksums, and false otherwise."""
try:
obj = self.target_s3.meta.client.head_object(Bucket=bucket, Key=key)
... | Returns true if the key already exists in the current bucket and the clientside checksum matches the
file's checksums, and false otherwise. | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/lib/s3_agent.py#L130-L141 |
HumanCellAtlas/dcp-cli | hca/dss/upload_to_cloud.py | upload_to_cloud | def upload_to_cloud(file_handles, staging_bucket, replica, from_cloud=False):
"""
Upload files to cloud.
:param file_handles: If from_cloud, file_handles is a aws s3 directory path to files with appropriate
metadata uploaded. Else, a list of binary file_handles to upload.
:para... | python | def upload_to_cloud(file_handles, staging_bucket, replica, from_cloud=False):
"""
Upload files to cloud.
:param file_handles: If from_cloud, file_handles is a aws s3 directory path to files with appropriate
metadata uploaded. Else, a list of binary file_handles to upload.
:para... | Upload files to cloud.
:param file_handles: If from_cloud, file_handles is a aws s3 directory path to files with appropriate
metadata uploaded. Else, a list of binary file_handles to upload.
:param staging_bucket: The aws bucket to upload the files to.
:param replica: The cloud rep... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/dss/upload_to_cloud.py#L53-L102 |
HumanCellAtlas/dcp-cli | hca/dss/__init__.py | DSSClient.download | def download(self, bundle_uuid, replica, version="", download_dir="",
metadata_files=('*',), data_files=('*',),
num_retries=10, min_delay_seconds=0.25):
"""
Download a bundle and save it to the local filesystem as a directory.
:param str bundle_uuid: The uuid o... | python | def download(self, bundle_uuid, replica, version="", download_dir="",
metadata_files=('*',), data_files=('*',),
num_retries=10, min_delay_seconds=0.25):
"""
Download a bundle and save it to the local filesystem as a directory.
:param str bundle_uuid: The uuid o... | Download a bundle and save it to the local filesystem as a directory.
:param str bundle_uuid: The uuid of the bundle to download
:param str replica: the replica to download from. The supported replicas are: `aws` for Amazon Web Services, and
`gcp` for Google Cloud Platform. [aws, gcp]
... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/dss/__init__.py#L87-L140 |
HumanCellAtlas/dcp-cli | hca/dss/__init__.py | DSSClient._download_to_filestore | def _download_to_filestore(self, download_dir, dss_file, num_retries=10, min_delay_seconds=0.25):
"""
Attempt to download the data and save it in the 'filestore' location dictated by self._file_path()
"""
dest_path = self._file_path(dss_file.sha256, download_dir)
if os.path.exist... | python | def _download_to_filestore(self, download_dir, dss_file, num_retries=10, min_delay_seconds=0.25):
"""
Attempt to download the data and save it in the 'filestore' location dictated by self._file_path()
"""
dest_path = self._file_path(dss_file.sha256, download_dir)
if os.path.exist... | Attempt to download the data and save it in the 'filestore' location dictated by self._file_path() | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/dss/__init__.py#L198-L209 |
HumanCellAtlas/dcp-cli | hca/dss/__init__.py | DSSClient._download_file | def _download_file(self, dss_file, dest_path, num_retries=10, min_delay_seconds=0.25):
"""
Attempt to download the data. If a retryable exception occurs, we wait a bit and retry again. The delay
increases each time we fail and decreases each time we successfully read a block. We set a quota f... | python | def _download_file(self, dss_file, dest_path, num_retries=10, min_delay_seconds=0.25):
"""
Attempt to download the data. If a retryable exception occurs, we wait a bit and retry again. The delay
increases each time we fail and decreases each time we successfully read a block. We set a quota f... | Attempt to download the data. If a retryable exception occurs, we wait a bit and retry again. The delay
increases each time we fail and decreases each time we successfully read a block. We set a quota for the
number of failures that goes up with every successful block read and down with each failure.... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/dss/__init__.py#L211-L237 |
HumanCellAtlas/dcp-cli | hca/dss/__init__.py | DSSClient._do_download_file | def _do_download_file(self, dss_file, fh, num_retries, min_delay_seconds):
"""
Abstracts away complications for downloading a file, handles retries and delays, and computes its hash
"""
hasher = hashlib.sha256()
delay = min_delay_seconds
retries_left = num_retries
... | python | def _do_download_file(self, dss_file, fh, num_retries, min_delay_seconds):
"""
Abstracts away complications for downloading a file, handles retries and delays, and computes its hash
"""
hasher = hashlib.sha256()
delay = min_delay_seconds
retries_left = num_retries
... | Abstracts away complications for downloading a file, handles retries and delays, and computes its hash | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/dss/__init__.py#L239-L303 |
HumanCellAtlas/dcp-cli | hca/dss/__init__.py | DSSClient._file_path | def _file_path(cls, checksum, download_dir):
"""
returns a file's relative local path based on the nesting parameters and the files hash
:param checksum: a string checksum
:param download_dir: root directory for filestore
:return: relative Path object
"""
checksum... | python | def _file_path(cls, checksum, download_dir):
"""
returns a file's relative local path based on the nesting parameters and the files hash
:param checksum: a string checksum
:param download_dir: root directory for filestore
:return: relative Path object
"""
checksum... | returns a file's relative local path based on the nesting parameters and the files hash
:param checksum: a string checksum
:param download_dir: root directory for filestore
:return: relative Path object | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/dss/__init__.py#L306-L322 |
HumanCellAtlas/dcp-cli | hca/dss/__init__.py | DSSClient._write_output_manifest | def _write_output_manifest(self, manifest, filestore_root):
"""
Adds the file path column to the manifest and writes the copy to the current directory. If the original manifest
is in the current directory it is overwritten with a warning.
"""
output = os.path.basename(manifest)
... | python | def _write_output_manifest(self, manifest, filestore_root):
"""
Adds the file path column to the manifest and writes the copy to the current directory. If the original manifest
is in the current directory it is overwritten with a warning.
"""
output = os.path.basename(manifest)
... | Adds the file path column to the manifest and writes the copy to the current directory. If the original manifest
is in the current directory it is overwritten with a warning. | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/dss/__init__.py#L332-L350 |
HumanCellAtlas/dcp-cli | hca/dss/__init__.py | DSSClient.download_manifest_v2 | def download_manifest_v2(self, manifest, replica,
num_retries=10,
min_delay_seconds=0.25,
download_dir='.'):
"""
Process the given manifest file in TSV (tab-separated values) format and download the files referenced b... | python | def download_manifest_v2(self, manifest, replica,
num_retries=10,
min_delay_seconds=0.25,
download_dir='.'):
"""
Process the given manifest file in TSV (tab-separated values) format and download the files referenced b... | Process the given manifest file in TSV (tab-separated values) format and download the files referenced by it.
The files are downloaded in the version 2 format.
This download format will serve as the main storage format for downloaded files. If a user specifies a different
format for download (c... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/dss/__init__.py#L352-L405 |
HumanCellAtlas/dcp-cli | hca/dss/__init__.py | DSSClient.download_manifest | def download_manifest(self, manifest, replica, num_retries=10, min_delay_seconds=0.25, download_dir=''):
"""
Process the given manifest file in TSV (tab-separated values) format and download the files referenced by it.
:param str manifest: path to a TSV (tab-separated values) file listing files... | python | def download_manifest(self, manifest, replica, num_retries=10, min_delay_seconds=0.25, download_dir=''):
"""
Process the given manifest file in TSV (tab-separated values) format and download the files referenced by it.
:param str manifest: path to a TSV (tab-separated values) file listing files... | Process the given manifest file in TSV (tab-separated values) format and download the files referenced by it.
:param str manifest: path to a TSV (tab-separated values) file listing files to download
:param str replica: the replica to download from. The supported replicas are: `aws` for Amazon Web Servi... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/dss/__init__.py#L407-L457 |
HumanCellAtlas/dcp-cli | hca/dss/__init__.py | DSSClient.upload | def upload(self, src_dir, replica, staging_bucket, timeout_seconds=1200):
"""
Upload a directory of files from the local filesystem and create a bundle containing the uploaded files.
:param str src_dir: file path to a directory of files to upload to the replica.
:param str replica: the ... | python | def upload(self, src_dir, replica, staging_bucket, timeout_seconds=1200):
"""
Upload a directory of files from the local filesystem and create a bundle containing the uploaded files.
:param str src_dir: file path to a directory of files to upload to the replica.
:param str replica: the ... | Upload a directory of files from the local filesystem and create a bundle containing the uploaded files.
:param str src_dir: file path to a directory of files to upload to the replica.
:param str replica: the replica to upload to. The supported replicas are: `aws` for Amazon Web Services, and
... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/dss/__init__.py#L486-L580 |
HumanCellAtlas/dcp-cli | hca/dss/util/__init__.py | iter_paths | def iter_paths(src_dir):
"""
Function that recursively locates files within folder
Note: scandir does not guarantee ordering
:param src_dir: string for directory to be parsed through
:return an iterable of DirEntry objects all files within the src_dir
"""
for x in scandir(os.path.join(src_d... | python | def iter_paths(src_dir):
"""
Function that recursively locates files within folder
Note: scandir does not guarantee ordering
:param src_dir: string for directory to be parsed through
:return an iterable of DirEntry objects all files within the src_dir
"""
for x in scandir(os.path.join(src_d... | Function that recursively locates files within folder
Note: scandir does not guarantee ordering
:param src_dir: string for directory to be parsed through
:return an iterable of DirEntry objects all files within the src_dir | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/dss/util/__init__.py#L15-L27 |
HumanCellAtlas/dcp-cli | hca/dss/util/__init__.py | hardlink | def hardlink(source, link_name):
"""
Create a hardlink in a portable way
The code for Windows support is adapted from:
https://github.com/sunshowers/ntfs/blob/master/ntfsutils/hardlink.py
"""
if sys.version_info < (3,) and platform.system() == 'Windows': # pragma: no cover
import ctype... | python | def hardlink(source, link_name):
"""
Create a hardlink in a portable way
The code for Windows support is adapted from:
https://github.com/sunshowers/ntfs/blob/master/ntfsutils/hardlink.py
"""
if sys.version_info < (3,) and platform.system() == 'Windows': # pragma: no cover
import ctype... | Create a hardlink in a portable way
The code for Windows support is adapted from:
https://github.com/sunshowers/ntfs/blob/master/ntfsutils/hardlink.py | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/dss/util/__init__.py#L40-L69 |
HumanCellAtlas/dcp-cli | hca/util/__init__.py | _ClientMethodFactory.request_with_retries_on_post_search | def request_with_retries_on_post_search(self, session, url, query, json_input, stream, headers):
"""
Submit a request and retry POST search requests specifically.
We don't currently retry on POST requests, and this is intended as a temporary fix until
the swagger is updated and changes ... | python | def request_with_retries_on_post_search(self, session, url, query, json_input, stream, headers):
"""
Submit a request and retry POST search requests specifically.
We don't currently retry on POST requests, and this is intended as a temporary fix until
the swagger is updated and changes ... | Submit a request and retry POST search requests specifically.
We don't currently retry on POST requests, and this is intended as a temporary fix until
the swagger is updated and changes applied to prod. In the meantime, this function will add
retries specifically for POST search (and any other... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/util/__init__.py#L143-L174 |
HumanCellAtlas/dcp-cli | hca/util/__init__.py | SwaggerClient.load_swagger_json | def load_swagger_json(swagger_json, ptr_str="$ref"):
"""
Load the Swagger JSON and resolve {"$ref": "#/..."} internal JSON Pointer references.
"""
refs = []
def store_refs(d):
if len(d) == 1 and ptr_str in d:
refs.append(d)
return d
... | python | def load_swagger_json(swagger_json, ptr_str="$ref"):
"""
Load the Swagger JSON and resolve {"$ref": "#/..."} internal JSON Pointer references.
"""
refs = []
def store_refs(d):
if len(d) == 1 and ptr_str in d:
refs.append(d)
return d
... | Load the Swagger JSON and resolve {"$ref": "#/..."} internal JSON Pointer references. | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/util/__init__.py#L286-L302 |
HumanCellAtlas/dcp-cli | hca/util/__init__.py | SwaggerClient.refresh_swagger | def refresh_swagger(self):
"""
Manually refresh the swagger document. This can help resolve errors communicate with the API.
"""
try:
os.remove(self._get_swagger_filename(self.swagger_url))
except EnvironmentError as e:
logger.warn(os.strerror(e.errno))
... | python | def refresh_swagger(self):
"""
Manually refresh the swagger document. This can help resolve errors communicate with the API.
"""
try:
os.remove(self._get_swagger_filename(self.swagger_url))
except EnvironmentError as e:
logger.warn(os.strerror(e.errno))
... | Manually refresh the swagger document. This can help resolve errors communicate with the API. | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/util/__init__.py#L335-L344 |
HumanCellAtlas/dcp-cli | hca/util/__init__.py | SwaggerClient.login | def login(self, access_token=""):
"""
Configure and save {prog} authentication credentials.
This command may open a browser window to ask for your
consent to use web service authentication credentials.
"""
if access_token:
credentials = argparse.Namespace(tok... | python | def login(self, access_token=""):
"""
Configure and save {prog} authentication credentials.
This command may open a browser window to ask for your
consent to use web service authentication credentials.
"""
if access_token:
credentials = argparse.Namespace(tok... | Configure and save {prog} authentication credentials.
This command may open a browser window to ask for your
consent to use web service authentication credentials. | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/util/__init__.py#L370-L393 |
HumanCellAtlas/dcp-cli | hca/upload/upload_config.py | UploadConfig.area_uri | def area_uri(self, area_uuid):
"""
Return the URI for an Upload Area
:param area_uuid: UUID of area for which we want URI
:return: Upload Area URI object
:rtype: UploadAreaURI
:raises UploadException: if area does not exist
"""
if area_uuid not in self.are... | python | def area_uri(self, area_uuid):
"""
Return the URI for an Upload Area
:param area_uuid: UUID of area for which we want URI
:return: Upload Area URI object
:rtype: UploadAreaURI
:raises UploadException: if area does not exist
"""
if area_uuid not in self.are... | Return the URI for an Upload Area
:param area_uuid: UUID of area for which we want URI
:return: Upload Area URI object
:rtype: UploadAreaURI
:raises UploadException: if area does not exist | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/upload_config.py#L85-L95 |
HumanCellAtlas/dcp-cli | hca/upload/upload_config.py | UploadConfig.add_area | def add_area(self, uri):
"""
Record information about a new Upload Area
:param UploadAreaURI uri: An Upload Area URI.
"""
if uri.area_uuid not in self._config.upload.areas:
self._config.upload.areas[uri.area_uuid] = {'uri': uri.uri}
self.save() | python | def add_area(self, uri):
"""
Record information about a new Upload Area
:param UploadAreaURI uri: An Upload Area URI.
"""
if uri.area_uuid not in self._config.upload.areas:
self._config.upload.areas[uri.area_uuid] = {'uri': uri.uri}
self.save() | Record information about a new Upload Area
:param UploadAreaURI uri: An Upload Area URI. | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/upload_config.py#L97-L105 |
HumanCellAtlas/dcp-cli | hca/upload/upload_config.py | UploadConfig.select_area | def select_area(self, area_uuid):
"""
Update the "current area" to be the area with this UUID.
:param str area_uuid: The RFC4122-compliant UUID of the Upload Area.
"""
self._config.upload.current_area = area_uuid
self.save() | python | def select_area(self, area_uuid):
"""
Update the "current area" to be the area with this UUID.
:param str area_uuid: The RFC4122-compliant UUID of the Upload Area.
"""
self._config.upload.current_area = area_uuid
self.save() | Update the "current area" to be the area with this UUID.
:param str area_uuid: The RFC4122-compliant UUID of the Upload Area. | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/upload_config.py#L107-L115 |
HumanCellAtlas/dcp-cli | hca/upload/upload_config.py | UploadConfig.forget_area | def forget_area(self, area_uuid):
"""
Remove an Upload Area from out cache of known areas.
:param str area_uuid: The RFC4122-compliant UUID of the Upload Area.
"""
if self._config.upload.current_area == area_uuid:
self._config.upload.current_area = None
if are... | python | def forget_area(self, area_uuid):
"""
Remove an Upload Area from out cache of known areas.
:param str area_uuid: The RFC4122-compliant UUID of the Upload Area.
"""
if self._config.upload.current_area == area_uuid:
self._config.upload.current_area = None
if are... | Remove an Upload Area from out cache of known areas.
:param str area_uuid: The RFC4122-compliant UUID of the Upload Area. | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/upload_config.py#L117-L126 |
HumanCellAtlas/dcp-cli | hca/upload/upload_config.py | UploadConfig.area_uuid_from_partial_uuid | def area_uuid_from_partial_uuid(self, partial_uuid):
"""
Given a partial UUID (a prefix), see if we have know about an Upload Area matching it.
:param (str) partial_uuid: UUID prefix
:return: a matching UUID
:rtype: str
:raises UploadException: if no or more than one UUID... | python | def area_uuid_from_partial_uuid(self, partial_uuid):
"""
Given a partial UUID (a prefix), see if we have know about an Upload Area matching it.
:param (str) partial_uuid: UUID prefix
:return: a matching UUID
:rtype: str
:raises UploadException: if no or more than one UUID... | Given a partial UUID (a prefix), see if we have know about an Upload Area matching it.
:param (str) partial_uuid: UUID prefix
:return: a matching UUID
:rtype: str
:raises UploadException: if no or more than one UUIDs match. | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/upload_config.py#L128-L143 |
HumanCellAtlas/dcp-cli | hca/upload/upload_config.py | UploadConfig.unique_prefix | def unique_prefix(self, area_uuid):
"""
Find the minimum prefix required to address this Upload Area UUID uniquely.
:param (str) area_uuid: UUID of Upload Area
:return: a string with the minimum prefix required to be unique
:rtype: str
"""
for prefix_len in range(... | python | def unique_prefix(self, area_uuid):
"""
Find the minimum prefix required to address this Upload Area UUID uniquely.
:param (str) area_uuid: UUID of Upload Area
:return: a string with the minimum prefix required to be unique
:rtype: str
"""
for prefix_len in range(... | Find the minimum prefix required to address this Upload Area UUID uniquely.
:param (str) area_uuid: UUID of Upload Area
:return: a string with the minimum prefix required to be unique
:rtype: str | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/upload_config.py#L145-L156 |
HumanCellAtlas/dcp-cli | hca/util/fs_helper.py | FSHelper.get_days_since_last_modified | def get_days_since_last_modified(filename):
"""
:param filename: Absolute file path
:return: Number of days since filename's last modified time
"""
now = datetime.now()
last_modified = datetime.fromtimestamp(os.path.getmtime(filename))
return (now - last_modified)... | python | def get_days_since_last_modified(filename):
"""
:param filename: Absolute file path
:return: Number of days since filename's last modified time
"""
now = datetime.now()
last_modified = datetime.fromtimestamp(os.path.getmtime(filename))
return (now - last_modified)... | :param filename: Absolute file path
:return: Number of days since filename's last modified time | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/util/fs_helper.py#L17-L24 |
HumanCellAtlas/dcp-cli | hca/upload/upload_service.py | UploadService.create_area | def create_area(self, area_uuid):
"""
Create an Upload Area
:param area_uuid: UUID of Upload Area to be created
:return: an Upload Area object
:rtype: UploadArea
"""
result = self.api_client.create_area(area_uuid=area_uuid)
area_uri = UploadAreaURI(uri=res... | python | def create_area(self, area_uuid):
"""
Create an Upload Area
:param area_uuid: UUID of Upload Area to be created
:return: an Upload Area object
:rtype: UploadArea
"""
result = self.api_client.create_area(area_uuid=area_uuid)
area_uri = UploadAreaURI(uri=res... | Create an Upload Area
:param area_uuid: UUID of Upload Area to be created
:return: an Upload Area object
:rtype: UploadArea | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/upload_service.py#L29-L38 |
HumanCellAtlas/dcp-cli | hca/upload/lib/api_client.py | ApiClient.create_area | def create_area(self, area_uuid):
"""
Create an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: a dict of the form { "uri": "s3://<bucket_name>/<upload-area-id>/" }
:rtype: dict
:raises UploadApiException: if the an Upload Area was n... | python | def create_area(self, area_uuid):
"""
Create an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: a dict of the form { "uri": "s3://<bucket_name>/<upload-area-id>/" }
:rtype: dict
:raises UploadApiException: if the an Upload Area was n... | Create an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: a dict of the form { "uri": "s3://<bucket_name>/<upload-area-id>/" }
:rtype: dict
:raises UploadApiException: if the an Upload Area was not created | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/lib/api_client.py#L35-L47 |
HumanCellAtlas/dcp-cli | hca/upload/lib/api_client.py | ApiClient.area_exists | def area_exists(self, area_uuid):
"""
Check if an Upload Area exists
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: True or False
:rtype: bool
"""
response = requests.head(self._url(path="/area/{id}".format(id=area_uuid)))
retur... | python | def area_exists(self, area_uuid):
"""
Check if an Upload Area exists
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: True or False
:rtype: bool
"""
response = requests.head(self._url(path="/area/{id}".format(id=area_uuid)))
retur... | Check if an Upload Area exists
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: True or False
:rtype: bool | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/lib/api_client.py#L49-L58 |
HumanCellAtlas/dcp-cli | hca/upload/lib/api_client.py | ApiClient.delete_area | def delete_area(self, area_uuid):
"""
Delete an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: True
:rtype: bool
:raises UploadApiException: if the an Upload Area was not deleted
"""
self._make_request('delete', path... | python | def delete_area(self, area_uuid):
"""
Delete an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: True
:rtype: bool
:raises UploadApiException: if the an Upload Area was not deleted
"""
self._make_request('delete', path... | Delete an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: True
:rtype: bool
:raises UploadApiException: if the an Upload Area was not deleted | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/lib/api_client.py#L60-L71 |
HumanCellAtlas/dcp-cli | hca/upload/lib/api_client.py | ApiClient.credentials | def credentials(self, area_uuid):
"""
Get AWS credentials required to directly upload files to Upload Area in S3
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: a dict containing an AWS AccessKey, SecretKey and SessionToken
:rtype: dict
:raises ... | python | def credentials(self, area_uuid):
"""
Get AWS credentials required to directly upload files to Upload Area in S3
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: a dict containing an AWS AccessKey, SecretKey and SessionToken
:rtype: dict
:raises ... | Get AWS credentials required to directly upload files to Upload Area in S3
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: a dict containing an AWS AccessKey, SecretKey and SessionToken
:rtype: dict
:raises UploadApiException: if credentials could not be obtain... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/lib/api_client.py#L73-L83 |
HumanCellAtlas/dcp-cli | hca/upload/lib/api_client.py | ApiClient.store_file | def store_file(self, area_uuid, filename, file_content, content_type):
"""
Store a small file in an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param str filename: The name the file will have in the Upload Area
:param str file_content: The conte... | python | def store_file(self, area_uuid, filename, file_content, content_type):
"""
Store a small file in an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param str filename: The name the file will have in the Upload Area
:param str file_content: The conte... | Store a small file in an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param str filename: The name the file will have in the Upload Area
:param str file_content: The contents of the file
:param str content_type: The MIME-type for the file
:return... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/lib/api_client.py#L87-L108 |
HumanCellAtlas/dcp-cli | hca/upload/lib/api_client.py | ApiClient.file_upload_notification | def file_upload_notification(self, area_uuid, filename):
"""
Notify Upload Service that a file has been placed in an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param str filename: The name the file in the Upload Area
:return: True
:rtyp... | python | def file_upload_notification(self, area_uuid, filename):
"""
Notify Upload Service that a file has been placed in an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param str filename: The name the file in the Upload Area
:return: True
:rtyp... | Notify Upload Service that a file has been placed in an Upload Area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param str filename: The name the file in the Upload Area
:return: True
:rtype: bool
:raises UploadApiException: if file could not be stored | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/lib/api_client.py#L111-L124 |
HumanCellAtlas/dcp-cli | hca/upload/lib/api_client.py | ApiClient.files_info | def files_info(self, area_uuid, file_list):
"""
Get information about files
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param list file_list: The names the files in the Upload Area about which we want information
:return: an array of file information dicts
... | python | def files_info(self, area_uuid, file_list):
"""
Get information about files
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param list file_list: The names the files in the Upload Area about which we want information
:return: an array of file information dicts
... | Get information about files
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param list file_list: The names the files in the Upload Area about which we want information
:return: an array of file information dicts
:rtype: list of dicts
:raises UploadApiException... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/lib/api_client.py#L126-L139 |
HumanCellAtlas/dcp-cli | hca/upload/lib/api_client.py | ApiClient.checksum_status | def checksum_status(self, area_uuid, filename):
"""
Retrieve checksum status and values for a file
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param str filename: The name of the file within the Upload Area
:return: a dict with checksum information
... | python | def checksum_status(self, area_uuid, filename):
"""
Retrieve checksum status and values for a file
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param str filename: The name of the file within the Upload Area
:return: a dict with checksum information
... | Retrieve checksum status and values for a file
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param str filename: The name of the file within the Upload Area
:return: a dict with checksum information
:rtype: dict
:raises UploadApiException: if information coul... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/lib/api_client.py#L143-L156 |
HumanCellAtlas/dcp-cli | hca/upload/lib/api_client.py | ApiClient.validate_files | def validate_files(self, area_uuid, file_list, validator_image, original_validation_id="", environment={}):
"""
Invoke supplied validator Docker image and give it access to the file/s.
The validator must be based off the base validator Docker image.
:param str area_uuid: A RFC4122-compl... | python | def validate_files(self, area_uuid, file_list, validator_image, original_validation_id="", environment={}):
"""
Invoke supplied validator Docker image and give it access to the file/s.
The validator must be based off the base validator Docker image.
:param str area_uuid: A RFC4122-compl... | Invoke supplied validator Docker image and give it access to the file/s.
The validator must be based off the base validator Docker image.
:param str area_uuid: A RFC4122-compliant ID for the upload area
:param list file_list: A list of files within the Upload Area to be validated
:param... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/lib/api_client.py#L174-L197 |
HumanCellAtlas/dcp-cli | hca/upload/lib/api_client.py | ApiClient.validation_statuses | def validation_statuses(self, area_uuid):
"""
Get count of validation statuses for all files in upload_area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: a dict with key for each state and value being the count of files in that state
:rtype: dict
... | python | def validation_statuses(self, area_uuid):
"""
Get count of validation statuses for all files in upload_area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: a dict with key for each state and value being the count of files in that state
:rtype: dict
... | Get count of validation statuses for all files in upload_area
:param str area_uuid: A RFC4122-compliant ID for the upload area
:return: a dict with key for each state and value being the count of files in that state
:rtype: dict
:raises UploadApiException: if information could not be ob... | https://github.com/HumanCellAtlas/dcp-cli/blob/cc70817bc4e50944c709eaae160de0bf7a19f0f3/hca/upload/lib/api_client.py#L214-L225 |
yoeo/guesslang | guesslang/guesser.py | Guess.language_name | def language_name(self, text: str) -> str:
"""Predict the programming language name of the given source code.
:param text: source code.
:return: language name
"""
values = extract(text)
input_fn = _to_func(([values], []))
pos: int = next(self._classifier.predict_... | python | def language_name(self, text: str) -> str:
"""Predict the programming language name of the given source code.
:param text: source code.
:return: language name
"""
values = extract(text)
input_fn = _to_func(([values], []))
pos: int = next(self._classifier.predict_... | Predict the programming language name of the given source code.
:param text: source code.
:return: language name | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/guesser.py#L61-L72 |
yoeo/guesslang | guesslang/guesser.py | Guess.scores | def scores(self, text: str) -> Dict[str, float]:
"""A score for each language corresponding to the probability that
the text is written in the given language.
The score is a `float` value between 0.0 and 1.0
:param text: source code.
:return: language to score dictionary
... | python | def scores(self, text: str) -> Dict[str, float]:
"""A score for each language corresponding to the probability that
the text is written in the given language.
The score is a `float` value between 0.0 and 1.0
:param text: source code.
:return: language to score dictionary
... | A score for each language corresponding to the probability that
the text is written in the given language.
The score is a `float` value between 0.0 and 1.0
:param text: source code.
:return: language to score dictionary | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/guesser.py#L74-L87 |
yoeo/guesslang | guesslang/guesser.py | Guess.probable_languages | def probable_languages(
self,
text: str,
max_languages: int = 3) -> Tuple[str, ...]:
"""List of most probable programming languages,
the list is ordered from the most probable to the least probable one.
:param text: source code.
:param max_languages: ... | python | def probable_languages(
self,
text: str,
max_languages: int = 3) -> Tuple[str, ...]:
"""List of most probable programming languages,
the list is ordered from the most probable to the least probable one.
:param text: source code.
:param max_languages: ... | List of most probable programming languages,
the list is ordered from the most probable to the least probable one.
:param text: source code.
:param max_languages: maximum number of listed languages.
:return: languages list | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/guesser.py#L89-L116 |
yoeo/guesslang | guesslang/guesser.py | Guess.learn | def learn(self, input_dir: str) -> float:
"""Learn languages features from source files.
:raise GuesslangError: when the default model is used for learning
:param input_dir: source code files directory.
:return: learning accuracy
"""
if self.is_default:
LOGGE... | python | def learn(self, input_dir: str) -> float:
"""Learn languages features from source files.
:raise GuesslangError: when the default model is used for learning
:param input_dir: source code files directory.
:return: learning accuracy
"""
if self.is_default:
LOGGE... | Learn languages features from source files.
:raise GuesslangError: when the default model is used for learning
:param input_dir: source code files directory.
:return: learning accuracy | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/guesser.py#L118-L164 |
yoeo/guesslang | tools/report_graph.py | main | def main():
"""Report graph creator command line"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
'reportfile', type=argparse.FileType('r'),
help="test report file generated by `guesslang --test TESTDIR`")
parser.add_argument(
'-d', '--debug', defaul... | python | def main():
"""Report graph creator command line"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
'reportfile', type=argparse.FileType('r'),
help="test report file generated by `guesslang --test TESTDIR`")
parser.add_argument(
'-d', '--debug', defaul... | Report graph creator command line | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/tools/report_graph.py#L25-L42 |
yoeo/guesslang | guesslang/utils.py | search_files | def search_files(source: str, extensions: List[str]) -> List[Path]:
"""Retrieve files located the source directory and its subdirectories,
whose extension match one of the listed extensions.
:raise GuesslangError: when there is not enough files in the directory
:param source: directory name
:param ... | python | def search_files(source: str, extensions: List[str]) -> List[Path]:
"""Retrieve files located the source directory and its subdirectories,
whose extension match one of the listed extensions.
:raise GuesslangError: when there is not enough files in the directory
:param source: directory name
:param ... | Retrieve files located the source directory and its subdirectories,
whose extension match one of the listed extensions.
:raise GuesslangError: when there is not enough files in the directory
:param source: directory name
:param extensions: list of file extensions
:return: filenames | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/utils.py#L30-L52 |
yoeo/guesslang | guesslang/utils.py | extract_from_files | def extract_from_files(
files: List[Path],
languages: Dict[str, List[str]]) -> DataSet:
"""Extract arrays of features from the given files.
:param files: list of paths
:param languages: language name =>
associated file extension list
:return: features
"""
enumerator = en... | python | def extract_from_files(
files: List[Path],
languages: Dict[str, List[str]]) -> DataSet:
"""Extract arrays of features from the given files.
:param files: list of paths
:param languages: language name =>
associated file extension list
:return: features
"""
enumerator = en... | Extract arrays of features from the given files.
:param files: list of paths
:param languages: language name =>
associated file extension list
:return: features | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/utils.py#L55-L73 |
yoeo/guesslang | guesslang/utils.py | safe_read_file | def safe_read_file(file_path: Path) -> str:
"""Read a text file. Several text encodings are tried until
the file content is correctly decoded.
:raise GuesslangError: when the file encoding is not supported
:param file_path: path to the input file
:return: text file content
"""
for encoding ... | python | def safe_read_file(file_path: Path) -> str:
"""Read a text file. Several text encodings are tried until
the file content is correctly decoded.
:raise GuesslangError: when the file encoding is not supported
:param file_path: path to the input file
:return: text file content
"""
for encoding ... | Read a text file. Several text encodings are tried until
the file content is correctly decoded.
:raise GuesslangError: when the file encoding is not supported
:param file_path: path to the input file
:return: text file content | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/utils.py#L106-L120 |
yoeo/guesslang | guesslang/config.py | config_logging | def config_logging(debug: bool = False) -> None:
"""Set-up application and `tensorflow` logging.
:param debug: show or hide debug messages
"""
if debug:
level = 'DEBUG'
tf_level = tf.logging.INFO
else:
level = 'INFO'
tf_level = tf.logging.ERROR
logging_config = ... | python | def config_logging(debug: bool = False) -> None:
"""Set-up application and `tensorflow` logging.
:param debug: show or hide debug messages
"""
if debug:
level = 'DEBUG'
tf_level = tf.logging.INFO
else:
level = 'INFO'
tf_level = tf.logging.ERROR
logging_config = ... | Set-up application and `tensorflow` logging.
:param debug: show or hide debug messages | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/config.py#L53-L70 |
yoeo/guesslang | guesslang/config.py | config_dict | def config_dict(name: str) -> Dict[str, Any]:
"""Load a JSON configuration dict from Guesslang config directory.
:param name: the JSON file name.
:return: configuration
"""
try:
content = resource_string(PACKAGE, DATADIR.format(name)).decode()
except DistributionNotFound as error:
... | python | def config_dict(name: str) -> Dict[str, Any]:
"""Load a JSON configuration dict from Guesslang config directory.
:param name: the JSON file name.
:return: configuration
"""
try:
content = resource_string(PACKAGE, DATADIR.format(name)).decode()
except DistributionNotFound as error:
... | Load a JSON configuration dict from Guesslang config directory.
:param name: the JSON file name.
:return: configuration | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/config.py#L73-L85 |
yoeo/guesslang | guesslang/config.py | model_info | def model_info(model_dir: Optional[str] = None) -> Tuple[str, bool]:
"""Retrieve Guesslang model directory name,
and tells if it is the default model.
:param model_dir: model location, if `None` default model is selected
:return: selected model directory with an indication
that the model is the... | python | def model_info(model_dir: Optional[str] = None) -> Tuple[str, bool]:
"""Retrieve Guesslang model directory name,
and tells if it is the default model.
:param model_dir: model location, if `None` default model is selected
:return: selected model directory with an indication
that the model is the... | Retrieve Guesslang model directory name,
and tells if it is the default model.
:param model_dir: model location, if `None` default model is selected
:return: selected model directory with an indication
that the model is the default or not | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/config.py#L88-L110 |
yoeo/guesslang | guesslang/config.py | ColorLogFormatter.format | def format(self, record: logging.LogRecord) -> str:
"""Format log records to produce colored messages.
:param record: log record
:return: log message
"""
if platform.system() != 'Linux': # Avoid funny logs on Windows & MacOS
return super().format(record)
re... | python | def format(self, record: logging.LogRecord) -> str:
"""Format log records to produce colored messages.
:param record: log record
:return: log message
"""
if platform.system() != 'Linux': # Avoid funny logs on Windows & MacOS
return super().format(record)
re... | Format log records to produce colored messages.
:param record: log record
:return: log message | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/config.py#L37-L50 |
yoeo/guesslang | tools/download_github_repo.py | main | def main():
"""Github repositories downloaded command line"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
'githubtoken',
help="Github OAuth token, see https://developer.github.com/v3/oauth/")
parser.add_argument('destination', help="location of the downloa... | python | def main():
"""Github repositories downloaded command line"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument(
'githubtoken',
help="Github OAuth token, see https://developer.github.com/v3/oauth/")
parser.add_argument('destination', help="location of the downloa... | Github repositories downloaded command line | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/tools/download_github_repo.py#L54-L87 |
yoeo/guesslang | tools/download_github_repo.py | retry | def retry(default=None):
"""Retry functions after failures"""
def decorator(func):
"""Retry decorator"""
@functools.wraps(func)
def _wrapper(*args, **kw):
for pos in range(1, MAX_RETRIES):
try:
return func(*args, **kw)
exc... | python | def retry(default=None):
"""Retry functions after failures"""
def decorator(func):
"""Retry decorator"""
@functools.wraps(func)
def _wrapper(*args, **kw):
for pos in range(1, MAX_RETRIES):
try:
return func(*args, **kw)
exc... | Retry functions after failures | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/tools/download_github_repo.py#L117-L140 |
yoeo/guesslang | tools/make_keywords.py | main | def main():
"""Keywords generator command line"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('learn', help="learning source codes directory")
parser.add_argument('keywords', help="output keywords file, JSON")
parser.add_argument(
'-n', '--nbkeywords', type=int... | python | def main():
"""Keywords generator command line"""
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument('learn', help="learning source codes directory")
parser.add_argument('keywords', help="output keywords file, JSON")
parser.add_argument(
'-n', '--nbkeywords', type=int... | Keywords generator command line | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/tools/make_keywords.py#L29-L87 |
yoeo/guesslang | guesslang/__main__.py | main | def main() -> None:
"""Run command line"""
try:
_real_main()
except GuesslangError as error:
LOGGER.critical("Failed: %s", error)
sys.exit(-1)
except KeyboardInterrupt:
LOGGER.critical("Cancelled!")
sys.exit(-2) | python | def main() -> None:
"""Run command line"""
try:
_real_main()
except GuesslangError as error:
LOGGER.critical("Failed: %s", error)
sys.exit(-1)
except KeyboardInterrupt:
LOGGER.critical("Cancelled!")
sys.exit(-2) | Run command line | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/__main__.py#L19-L28 |
yoeo/guesslang | guesslang/extractor.py | split | def split(text: str) -> List[str]:
"""Split a text into a list of tokens.
:param text: the text to split
:return: tokens
"""
return [word for word in SEPARATOR.split(text) if word.strip(' \t')] | python | def split(text: str) -> List[str]:
"""Split a text into a list of tokens.
:param text: the text to split
:return: tokens
"""
return [word for word in SEPARATOR.split(text) if word.strip(' \t')] | Split a text into a list of tokens.
:param text: the text to split
:return: tokens | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/guesslang/extractor.py#L34-L40 |
yoeo/guesslang | tools/unzip_repos.py | main | def main():
"""Files extractor command line"""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('source', help="location of the downloaded repos")
parser.add_argument('destination', help="location of the ext... | python | def main():
"""Files extractor command line"""
parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.RawDescriptionHelpFormatter)
parser.add_argument('source', help="location of the downloaded repos")
parser.add_argument('destination', help="location of the ext... | Files extractor command line | https://github.com/yoeo/guesslang/blob/03e33b77c73238c0fe4600147e8c926515a2887f/tools/unzip_repos.py#L30-L65 |
innolitics/dicom-numpy | dicom_numpy/combine_slices.py | combine_slices | def combine_slices(slice_datasets, rescale=None):
'''
Given a list of pydicom datasets for an image series, stitch them together into a
three-dimensional numpy array. Also calculate a 4x4 affine transformation
matrix that converts the ijk-pixel-indices into the xyz-coordinates in the
DICOM patient'... | python | def combine_slices(slice_datasets, rescale=None):
'''
Given a list of pydicom datasets for an image series, stitch them together into a
three-dimensional numpy array. Also calculate a 4x4 affine transformation
matrix that converts the ijk-pixel-indices into the xyz-coordinates in the
DICOM patient'... | Given a list of pydicom datasets for an image series, stitch them together into a
three-dimensional numpy array. Also calculate a 4x4 affine transformation
matrix that converts the ijk-pixel-indices into the xyz-coordinates in the
DICOM patient's coordinate system.
Returns a two-tuple containing the 3... | https://github.com/innolitics/dicom-numpy/blob/c870f0302276e7eaa0b66e641bacee19fe090296/dicom_numpy/combine_slices.py#L12-L74 |
innolitics/dicom-numpy | dicom_numpy/combine_slices.py | _validate_slices_form_uniform_grid | def _validate_slices_form_uniform_grid(slice_datasets):
'''
Perform various data checks to ensure that the list of slices form a
evenly-spaced grid of data.
Some of these checks are probably not required if the data follows the
DICOM specification, however it seems pertinent to check anyway.
'''... | python | def _validate_slices_form_uniform_grid(slice_datasets):
'''
Perform various data checks to ensure that the list of slices form a
evenly-spaced grid of data.
Some of these checks are probably not required if the data follows the
DICOM specification, however it seems pertinent to check anyway.
'''... | Perform various data checks to ensure that the list of slices form a
evenly-spaced grid of data.
Some of these checks are probably not required if the data follows the
DICOM specification, however it seems pertinent to check anyway. | https://github.com/innolitics/dicom-numpy/blob/c870f0302276e7eaa0b66e641bacee19fe090296/dicom_numpy/combine_slices.py#L126-L153 |
innolitics/dicom-numpy | dicom_numpy/combine_slices.py | _validate_image_orientation | def _validate_image_orientation(image_orientation):
'''
Ensure that the image orientation is supported
- The direction cosines have magnitudes of 1 (just in case)
- The direction cosines are perpendicular
'''
row_cosine, column_cosine, slice_cosine = _extract_cosines(image_orientation)
if n... | python | def _validate_image_orientation(image_orientation):
'''
Ensure that the image orientation is supported
- The direction cosines have magnitudes of 1 (just in case)
- The direction cosines are perpendicular
'''
row_cosine, column_cosine, slice_cosine = _extract_cosines(image_orientation)
if n... | Ensure that the image orientation is supported
- The direction cosines have magnitudes of 1 (just in case)
- The direction cosines are perpendicular | https://github.com/innolitics/dicom-numpy/blob/c870f0302276e7eaa0b66e641bacee19fe090296/dicom_numpy/combine_slices.py#L156-L177 |
edx/opaque-keys | opaque_keys/edx/locator.py | BlockLocatorBase.parse_url | def parse_url(cls, string): # pylint: disable=redefined-outer-name
"""
If it can be parsed as a version_guid with no preceding org + offering, returns a dict
with key 'version_guid' and the value,
If it can be parsed as a org + offering, returns a dict
with key 'id' and optiona... | python | def parse_url(cls, string): # pylint: disable=redefined-outer-name
"""
If it can be parsed as a version_guid with no preceding org + offering, returns a dict
with key 'version_guid' and the value,
If it can be parsed as a org + offering, returns a dict
with key 'id' and optiona... | If it can be parsed as a version_guid with no preceding org + offering, returns a dict
with key 'version_guid' and the value,
If it can be parsed as a org + offering, returns a dict
with key 'id' and optional keys 'branch' and 'version_guid'.
Raises:
InvalidKeyError: if str... | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L110-L124 |
edx/opaque-keys | opaque_keys/edx/locator.py | CourseLocator.offering | def offering(self):
"""
Deprecated. Use course and run independently.
"""
warnings.warn(
"Offering is no longer a supported property of Locator. Please use the course and run properties.",
DeprecationWarning,
stacklevel=2
)
if not self.... | python | def offering(self):
"""
Deprecated. Use course and run independently.
"""
warnings.warn(
"Offering is no longer a supported property of Locator. Please use the course and run properties.",
DeprecationWarning,
stacklevel=2
)
if not self.... | Deprecated. Use course and run independently. | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L234-L247 |
edx/opaque-keys | opaque_keys/edx/locator.py | CourseLocator._from_string | def _from_string(cls, serialized):
"""
Return a CourseLocator parsing the given serialized string
:param serialized: matches the string to a CourseLocator
"""
parse = cls.parse_url(serialized)
if parse['version_guid']:
parse['version_guid'] = cls.as_object_id... | python | def _from_string(cls, serialized):
"""
Return a CourseLocator parsing the given serialized string
:param serialized: matches the string to a CourseLocator
"""
parse = cls.parse_url(serialized)
if parse['version_guid']:
parse['version_guid'] = cls.as_object_id... | Return a CourseLocator parsing the given serialized string
:param serialized: matches the string to a CourseLocator | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L250-L260 |
edx/opaque-keys | opaque_keys/edx/locator.py | CourseLocator.make_usage_key_from_deprecated_string | def make_usage_key_from_deprecated_string(self, location_url):
"""
Deprecated mechanism for creating a UsageKey given a CourseKey and a serialized Location.
NOTE: this prejudicially takes the tag, org, and course from the url not self.
Raises:
InvalidKeyError: if the url do... | python | def make_usage_key_from_deprecated_string(self, location_url):
"""
Deprecated mechanism for creating a UsageKey given a CourseKey and a serialized Location.
NOTE: this prejudicially takes the tag, org, and course from the url not self.
Raises:
InvalidKeyError: if the url do... | Deprecated mechanism for creating a UsageKey given a CourseKey and a serialized Location.
NOTE: this prejudicially takes the tag, org, and course from the url not self.
Raises:
InvalidKeyError: if the url does not parse | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L283-L297 |
edx/opaque-keys | opaque_keys/edx/locator.py | CourseLocator._to_deprecated_string | def _to_deprecated_string(self):
"""Returns an 'old-style' course id, represented as 'org/course/run'"""
return u'/'.join([self.org, self.course, self.run]) | python | def _to_deprecated_string(self):
"""Returns an 'old-style' course id, represented as 'org/course/run'"""
return u'/'.join([self.org, self.course, self.run]) | Returns an 'old-style' course id, represented as 'org/course/run | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L348-L350 |
edx/opaque-keys | opaque_keys/edx/locator.py | CourseLocator._from_deprecated_string | def _from_deprecated_string(cls, serialized):
"""
Return an instance of `cls` parsed from its deprecated `serialized` form.
This will be called only if :meth:`OpaqueKey.from_string` is unable to
parse a key out of `serialized`, and only if `set_deprecated_fallback` has
been call... | python | def _from_deprecated_string(cls, serialized):
"""
Return an instance of `cls` parsed from its deprecated `serialized` form.
This will be called only if :meth:`OpaqueKey.from_string` is unable to
parse a key out of `serialized`, and only if `set_deprecated_fallback` has
been call... | Return an instance of `cls` parsed from its deprecated `serialized` form.
This will be called only if :meth:`OpaqueKey.from_string` is unable to
parse a key out of `serialized`, and only if `set_deprecated_fallback` has
been called to register a fallback class.
Args:
cls: T... | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L362-L381 |
edx/opaque-keys | opaque_keys/edx/locator.py | LibraryLocator.for_branch | def for_branch(self, branch):
"""
Return a new CourseLocator for another branch of the same library (also version agnostic)
"""
if self.org is None and branch is not None:
raise InvalidKeyError(self.__class__, "Branches must have full library ids not just versions")
r... | python | def for_branch(self, branch):
"""
Return a new CourseLocator for another branch of the same library (also version agnostic)
"""
if self.org is None and branch is not None:
raise InvalidKeyError(self.__class__, "Branches must have full library ids not just versions")
r... | Return a new CourseLocator for another branch of the same library (also version agnostic) | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L545-L551 |
edx/opaque-keys | opaque_keys/edx/locator.py | LibraryLocator._to_string | def _to_string(self):
"""
Return a string representing this location.
"""
parts = []
if self.library: # pylint: disable=no-member
parts.extend([self.org, self.library]) # pylint: disable=no-member
if self.branch: # pylint: disable=no-member
... | python | def _to_string(self):
"""
Return a string representing this location.
"""
parts = []
if self.library: # pylint: disable=no-member
parts.extend([self.org, self.library]) # pylint: disable=no-member
if self.branch: # pylint: disable=no-member
... | Return a string representing this location. | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L560-L571 |
edx/opaque-keys | opaque_keys/edx/locator.py | BlockUsageLocator._from_string | def _from_string(cls, serialized):
"""
Requests CourseLocator to deserialize its part and then adds the local deserialization of block
"""
# Allow access to _from_string protected method
course_key = CourseLocator._from_string(serialized) # pylint: disable=protected-access
... | python | def _from_string(cls, serialized):
"""
Requests CourseLocator to deserialize its part and then adds the local deserialization of block
"""
# Allow access to _from_string protected method
course_key = CourseLocator._from_string(serialized) # pylint: disable=protected-access
... | Requests CourseLocator to deserialize its part and then adds the local deserialization of block | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L720-L730 |
edx/opaque-keys | opaque_keys/edx/locator.py | BlockUsageLocator.for_branch | def for_branch(self, branch):
"""
Return a UsageLocator for the same block in a different branch of the course.
"""
return self.replace(course_key=self.course_key.for_branch(branch)) | python | def for_branch(self, branch):
"""
Return a UsageLocator for the same block in a different branch of the course.
"""
return self.replace(course_key=self.course_key.for_branch(branch)) | Return a UsageLocator for the same block in a different branch of the course. | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L753-L757 |
edx/opaque-keys | opaque_keys/edx/locator.py | BlockUsageLocator.for_version | def for_version(self, version_guid):
"""
Return a UsageLocator for the same block in a different branch of the course.
"""
return self.replace(course_key=self.course_key.for_version(version_guid)) | python | def for_version(self, version_guid):
"""
Return a UsageLocator for the same block in a different branch of the course.
"""
return self.replace(course_key=self.course_key.for_version(version_guid)) | Return a UsageLocator for the same block in a different branch of the course. | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L759-L763 |
edx/opaque-keys | opaque_keys/edx/locator.py | BlockUsageLocator._parse_block_ref | def _parse_block_ref(cls, block_ref, deprecated=False):
"""
Given `block_ref`, tries to parse it into a valid block reference.
Returns `block_ref` if it is valid.
Raises:
InvalidKeyError: if `block_ref` is invalid.
"""
if deprecated and block_ref is None:
... | python | def _parse_block_ref(cls, block_ref, deprecated=False):
"""
Given `block_ref`, tries to parse it into a valid block reference.
Returns `block_ref` if it is valid.
Raises:
InvalidKeyError: if `block_ref` is invalid.
"""
if deprecated and block_ref is None:
... | Given `block_ref`, tries to parse it into a valid block reference.
Returns `block_ref` if it is valid.
Raises:
InvalidKeyError: if `block_ref` is invalid. | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L766-L788 |
edx/opaque-keys | opaque_keys/edx/locator.py | BlockUsageLocator.make_relative | def make_relative(cls, course_locator, block_type, block_id):
"""
Return a new instance which has the given block_id in the given course
:param course_locator: may be a BlockUsageLocator in the same snapshot
"""
if hasattr(course_locator, 'course_key'):
course_locator... | python | def make_relative(cls, course_locator, block_type, block_id):
"""
Return a new instance which has the given block_id in the given course
:param course_locator: may be a BlockUsageLocator in the same snapshot
"""
if hasattr(course_locator, 'course_key'):
course_locator... | Return a new instance which has the given block_id in the given course
:param course_locator: may be a BlockUsageLocator in the same snapshot | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L898-L908 |
edx/opaque-keys | opaque_keys/edx/locator.py | BlockUsageLocator._to_string | def _to_string(self):
"""
Return a string representing this location.
"""
# Allow access to _to_string protected method
return u"{course_key}+{BLOCK_TYPE_PREFIX}@{block_type}+{BLOCK_PREFIX}@{block_id}".format(
course_key=self.course_key._to_string(), # pylint: disabl... | python | def _to_string(self):
"""
Return a string representing this location.
"""
# Allow access to _to_string protected method
return u"{course_key}+{BLOCK_TYPE_PREFIX}@{block_type}+{BLOCK_PREFIX}@{block_id}".format(
course_key=self.course_key._to_string(), # pylint: disabl... | Return a string representing this location. | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L917-L928 |
edx/opaque-keys | opaque_keys/edx/locator.py | BlockUsageLocator.html_id | def html_id(self):
"""
Return an id which can be used on an html page as an id attr of an html element. It is currently also
persisted by some clients to identify blocks.
To make compatible with old Location object functionality. I don't believe this behavior fits at this
place... | python | def html_id(self):
"""
Return an id which can be used on an html page as an id attr of an html element. It is currently also
persisted by some clients to identify blocks.
To make compatible with old Location object functionality. I don't believe this behavior fits at this
place... | Return an id which can be used on an html page as an id attr of an html element. It is currently also
persisted by some clients to identify blocks.
To make compatible with old Location object functionality. I don't believe this behavior fits at this
place, but I have no way to override. We sho... | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L930-L944 |
edx/opaque-keys | opaque_keys/edx/locator.py | BlockUsageLocator._to_deprecated_string | def _to_deprecated_string(self):
"""
Returns an old-style location, represented as:
i4x://org/course/category/name[@revision] # Revision is optional
"""
# pylint: disable=missing-format-attribute
url = u"{0.DEPRECATED_TAG}://{0.course_key.org}/{0.course_key.course}/{0.bl... | python | def _to_deprecated_string(self):
"""
Returns an old-style location, represented as:
i4x://org/course/category/name[@revision] # Revision is optional
"""
# pylint: disable=missing-format-attribute
url = u"{0.DEPRECATED_TAG}://{0.course_key.org}/{0.course_key.course}/{0.bl... | Returns an old-style location, represented as:
i4x://org/course/category/name[@revision] # Revision is optional | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L946-L955 |
edx/opaque-keys | opaque_keys/edx/locator.py | BlockUsageLocator._from_deprecated_string | def _from_deprecated_string(cls, serialized):
"""
Return an instance of `cls` parsed from its deprecated `serialized` form.
This will be called only if :meth:`OpaqueKey.from_string` is unable to
parse a key out of `serialized`, and only if `set_deprecated_fallback` has
been call... | python | def _from_deprecated_string(cls, serialized):
"""
Return an instance of `cls` parsed from its deprecated `serialized` form.
This will be called only if :meth:`OpaqueKey.from_string` is unable to
parse a key out of `serialized`, and only if `set_deprecated_fallback` has
been call... | Return an instance of `cls` parsed from its deprecated `serialized` form.
This will be called only if :meth:`OpaqueKey.from_string` is unable to
parse a key out of `serialized`, and only if `set_deprecated_fallback` has
been called to register a fallback class.
Args:
cls: T... | https://github.com/edx/opaque-keys/blob/9807168660c12e0551c8fdd58fd1bc6b0bcb0a54/opaque_keys/edx/locator.py#L967-L994 |
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