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yougov/solr-doc-manager | mongo_connector/doc_managers/solr_doc_manager.py | DocManager._build_fields | def _build_fields(self):
""" Builds a list of valid fields
"""
declared_fields = self.solr._send_request('get', ADMIN_URL)
result = decoder.decode(declared_fields)
self.field_list = self._parse_fields(result, 'fields')
# Build regular expressions to match dynamic fields.... | python | def _build_fields(self):
""" Builds a list of valid fields
"""
declared_fields = self.solr._send_request('get', ADMIN_URL)
result = decoder.decode(declared_fields)
self.field_list = self._parse_fields(result, 'fields')
# Build regular expressions to match dynamic fields.... | [
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yougov/solr-doc-manager | mongo_connector/doc_managers/solr_doc_manager.py | DocManager._clean_doc | def _clean_doc(self, doc, namespace, timestamp):
"""Reformats the given document before insertion into Solr.
This method reformats the document in the following ways:
- removes extraneous fields that aren't defined in schema.xml
- unwinds arrays in order to find and later flatten su... | python | def _clean_doc(self, doc, namespace, timestamp):
"""Reformats the given document before insertion into Solr.
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yougov/solr-doc-manager | mongo_connector/doc_managers/solr_doc_manager.py | DocManager.apply_update | def apply_update(self, doc, update_spec):
"""Override DocManagerBase.apply_update to have flat documents."""
# Replace a whole document
if not '$set' in update_spec and not '$unset' in update_spec:
# update_spec contains the new document.
# Update the key in Solr based on... | python | def apply_update(self, doc, update_spec):
"""Override DocManagerBase.apply_update to have flat documents."""
# Replace a whole document
if not '$set' in update_spec and not '$unset' in update_spec:
# update_spec contains the new document.
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yougov/solr-doc-manager | mongo_connector/doc_managers/solr_doc_manager.py | DocManager.update | def update(self, document_id, update_spec, namespace, timestamp):
"""Apply updates given in update_spec to the document whose id
matches that of doc.
"""
# Commit outstanding changes so that the document to be updated is the
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"""Apply updates given in update_spec to the document whose id
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"""
# Commit outstanding changes so that the document to be updated is the
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yougov/solr-doc-manager | mongo_connector/doc_managers/solr_doc_manager.py | DocManager.upsert | def upsert(self, doc, namespace, timestamp):
"""Update or insert a document into Solr
This method should call whatever add/insert/update method exists for
the backend engine and add the document in there. The input will
always be one mongo document, represented as a Python dictionary.
... | python | def upsert(self, doc, namespace, timestamp):
"""Update or insert a document into Solr
This method should call whatever add/insert/update method exists for
the backend engine and add the document in there. The input will
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yougov/solr-doc-manager | mongo_connector/doc_managers/solr_doc_manager.py | DocManager.bulk_upsert | def bulk_upsert(self, docs, namespace, timestamp):
"""Update or insert multiple documents into Solr
docs may be any iterable
"""
if self.auto_commit_interval is not None:
add_kwargs = {
"commit": (self.auto_commit_interval == 0),
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"""Update or insert multiple documents into Solr
docs may be any iterable
"""
if self.auto_commit_interval is not None:
add_kwargs = {
"commit": (self.auto_commit_interval == 0),
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yougov/solr-doc-manager | mongo_connector/doc_managers/solr_doc_manager.py | DocManager.remove | def remove(self, document_id, namespace, timestamp):
"""Removes documents from Solr
The input is a python dictionary that represents a mongo document.
"""
self.solr.delete(id=u(document_id),
commit=(self.auto_commit_interval == 0)) | python | def remove(self, document_id, namespace, timestamp):
"""Removes documents from Solr
The input is a python dictionary that represents a mongo document.
"""
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yougov/solr-doc-manager | mongo_connector/doc_managers/solr_doc_manager.py | DocManager._stream_search | def _stream_search(self, query):
"""Helper method for iterating over Solr search results."""
for doc in self.solr.search(query, rows=100000000):
if self.unique_key != "_id":
doc["_id"] = doc.pop(self.unique_key)
yield doc | python | def _stream_search(self, query):
"""Helper method for iterating over Solr search results."""
for doc in self.solr.search(query, rows=100000000):
if self.unique_key != "_id":
doc["_id"] = doc.pop(self.unique_key)
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yougov/solr-doc-manager | mongo_connector/doc_managers/solr_doc_manager.py | DocManager.search | def search(self, start_ts, end_ts):
"""Called to query Solr for documents in a time range."""
query = '_ts: [%s TO %s]' % (start_ts, end_ts)
return self._stream_search(query) | python | def search(self, start_ts, end_ts):
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yougov/solr-doc-manager | mongo_connector/doc_managers/solr_doc_manager.py | DocManager.get_last_doc | def get_last_doc(self):
"""Returns the last document stored in the Solr engine.
"""
#search everything, sort by descending timestamp, return 1 row
try:
result = self.solr.search('*:*', sort='_ts desc', rows=1)
except ValueError:
return None
for r ... | python | def get_last_doc(self):
"""Returns the last document stored in the Solr engine.
"""
#search everything, sort by descending timestamp, return 1 row
try:
result = self.solr.search('*:*', sort='_ts desc', rows=1)
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return None
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ricmoo/pyscrypt | pyscrypt/hash.py | pbkdf2_single | def pbkdf2_single(password, salt, key_length, prf):
'''Returns the result of the Password-Based Key Derivation Function 2 with
a single iteration (i.e. count = 1).
prf - a psuedorandom function
See http://en.wikipedia.org/wiki/PBKDF2
'''
block_number = 0
result = b''
# The i... | python | def pbkdf2_single(password, salt, key_length, prf):
'''Returns the result of the Password-Based Key Derivation Function 2 with
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prf - a psuedorandom function
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ricmoo/pyscrypt | pyscrypt/hash.py | salsa20_8 | def salsa20_8(B):
'''Salsa 20/8 stream cypher; Used by BlockMix. See http://en.wikipedia.org/wiki/Salsa20'''
# Create a working copy
x = B[:]
# Expanded form of this code. The expansion is significantly faster but
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# ROUNDS = (
# (4, 0, 12, 7), (8, ... | python | def salsa20_8(B):
'''Salsa 20/8 stream cypher; Used by BlockMix. See http://en.wikipedia.org/wiki/Salsa20'''
# Create a working copy
x = B[:]
# Expanded form of this code. The expansion is significantly faster but
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ricmoo/pyscrypt | pyscrypt/hash.py | blockmix_salsa8 | def blockmix_salsa8(BY, Yi, r):
'''Blockmix; Used by SMix.'''
start = (2 * r - 1) * 16
X = BY[start:start + 16] # BlockMix - 1
for i in xrange(0, 2 * r): # BlockMix - 2
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'''Blockmix; Used by SMix.'''
start = (2 * r - 1) * 16
X = BY[start:start + 16] # BlockMix - 1
for i in xrange(0, 2 * r): # BlockMix - 2
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ricmoo/pyscrypt | pyscrypt/hash.py | smix | def smix(B, Bi, r, N, V, X):
'''SMix; a specific case of ROMix. See scrypt.pdf in the links above.'''
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aod = i * 32 * r # ROMix - 3
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'''SMix; a specific case of ROMix. See scrypt.pdf in the links above.'''
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ricmoo/pyscrypt | pyscrypt/hash.py | hash | def hash(password, salt, N, r, p, dkLen):
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r * p < (2 ** 30)
dkLen <= (((2 ** 32) - 1) * 32
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Constraints:
r * p < (2 ** 30)
dkLen <= (((2 ** 32) - 1) * 32
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ricmoo/pyscrypt | pyscrypt/file.py | ScryptFile._load_get_attr | def _load_get_attr(self, name):
'Return an internal attribute after ensuring the headers is loaded if necessary.'
if self._mode in _allowed_read and self._N is None:
self._read_header()
return getattr(self, name) | python | def _load_get_attr(self, name):
'Return an internal attribute after ensuring the headers is loaded if necessary.'
if self._mode in _allowed_read and self._N is None:
self._read_header()
return getattr(self, name) | [
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ricmoo/pyscrypt | pyscrypt/file.py | ScryptFile.close | def close(self):
'''Close the underlying file.
Sets data attribute .closed to True. A closed file cannot be used for
further I/O operations. close() may be called more than once without
error. Some kinds of file objects (for example, opened by popen())
may return an exit status ... | python | def close(self):
'''Close the underlying file.
Sets data attribute .closed to True. A closed file cannot be used for
further I/O operations. close() may be called more than once without
error. Some kinds of file objects (for example, opened by popen())
may return an exit status ... | [
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ricmoo/pyscrypt | pyscrypt/file.py | ScryptFile.verify_file | def verify_file(fp, password):
'Returns whether a scrypt encrypted file is valid.'
sf = ScryptFile(fp = fp, password = password)
for line in sf: pass
sf.close()
return sf.valid | python | def verify_file(fp, password):
'Returns whether a scrypt encrypted file is valid.'
sf = ScryptFile(fp = fp, password = password)
for line in sf: pass
sf.close()
return sf.valid | [
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ricmoo/pyscrypt | pyscrypt/file.py | ScryptFile.readline | def readline(self, size = None):
'''Next line from the decrypted file, as a string.
Retain newline. A non-negative size argument limits the maximum
number of bytes to return (an incomplete line may be returned then).
Return an empty string at EOF.'''
if self.closed: raise Valu... | python | def readline(self, size = None):
'''Next line from the decrypted file, as a string.
Retain newline. A non-negative size argument limits the maximum
number of bytes to return (an incomplete line may be returned then).
Return an empty string at EOF.'''
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ricmoo/pyscrypt | pyscrypt/file.py | ScryptFile._read_header | def _read_header(self):
'''Read and parse the header and calculate derived keys.'''
try:
# Read the entire header
header = self._fp.read(96)
if len(header) != 96:
raise InvalidScryptFileFormat("Incomplete header")
# Magic number
... | python | def _read_header(self):
'''Read and parse the header and calculate derived keys.'''
try:
# Read the entire header
header = self._fp.read(96)
if len(header) != 96:
raise InvalidScryptFileFormat("Incomplete header")
# Magic number
... | [
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ricmoo/pyscrypt | pyscrypt/file.py | ScryptFile.read | def read(self, size = None):
'''Read at most size bytes, returned as a string.
If the size argument is negative or omitted, read until EOF is reached.
Notice that when in non-blocking mode, less data than what was requested
may be returned, even if no size parameter was given.'''
... | python | def read(self, size = None):
'''Read at most size bytes, returned as a string.
If the size argument is negative or omitted, read until EOF is reached.
Notice that when in non-blocking mode, less data than what was requested
may be returned, even if no size parameter was given.'''
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ricmoo/pyscrypt | pyscrypt/file.py | ScryptFile._write_header | def _write_header(self):
'Writes the header to the underlying file object.'
header = b'scrypt' + CHR0 + struct.pack('>BII', int(math.log(self.N, 2)), self.r, self.p) + self.salt
# Add the header checksum to the header
checksum = hashlib.sha256(header).digest()[:16]
header += ch... | python | def _write_header(self):
'Writes the header to the underlying file object.'
header = b'scrypt' + CHR0 + struct.pack('>BII', int(math.log(self.N, 2)), self.r, self.p) + self.salt
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ricmoo/pyscrypt | pyscrypt/file.py | ScryptFile._finalize_write | def _finalize_write(self):
'Finishes any unencrypted bytes and writes the final checksum.'
# Make sure we have written the header
if not self._done_header:
self._write_header()
# Write the remaining decrypted part to disk
block = self._crypto.encrypt(self._decrypted... | python | def _finalize_write(self):
'Finishes any unencrypted bytes and writes the final checksum.'
# Make sure we have written the header
if not self._done_header:
self._write_header()
# Write the remaining decrypted part to disk
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ricmoo/pyscrypt | pyscrypt/file.py | ScryptFile.write | def write(self, str):
'''Write string str to the underlying file.
Note that due to buffering, flush() or close() may be needed before
the file on disk reflects the data written.'''
if self.closed: raise ValueError('File closed')
if self._mode in _allowed_read:
raise... | python | def write(self, str):
'''Write string str to the underlying file.
Note that due to buffering, flush() or close() may be needed before
the file on disk reflects the data written.'''
if self.closed: raise ValueError('File closed')
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dnanhkhoa/logone | logone/__init__.py | get_logger | def get_logger(logger_name):
"""
Return a logger with the specified name, creating it if necessary.
"""
# Use default global logger
if logger_name is None:
return __instance
assert isinstance(logger_name, str), 'Logger name must be a string!'
with __lock:
if logger_name in... | python | def get_logger(logger_name):
"""
Return a logger with the specified name, creating it if necessary.
"""
# Use default global logger
if logger_name is None:
return __instance
assert isinstance(logger_name, str), 'Logger name must be a string!'
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mikemelch/hallie | hallie/modules/files.py | removeFile | def removeFile(file):
"""remove a file"""
if "y" in speech.question("Are you sure you want to remove " + file + "? (Y/N): "):
speech.speak("Removing " + file + " with the 'rm' command.")
subprocess.call(["rm", "-r", file])
else:
speech.speak("Okay, I won't remove " + file + ".") | python | def removeFile(file):
"""remove a file"""
if "y" in speech.question("Are you sure you want to remove " + file + "? (Y/N): "):
speech.speak("Removing " + file + " with the 'rm' command.")
subprocess.call(["rm", "-r", file])
else:
speech.speak("Okay, I won't remove " + file + ".") | [
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mikemelch/hallie | hallie/modules/files.py | copy | def copy(location):
"""copy file or directory at a given location; can be pasted later"""
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copyFileLocation = os.path.abspath(location)
copy = {"copyLocation": copyFileLocation}
dataFile = open(copyData, "wb")
pickle.dump(copy, dataFile)
speech.speak(location + " copied successfu... | python | def copy(location):
"""copy file or directory at a given location; can be pasted later"""
copyData = settings.getDataFile()
copyFileLocation = os.path.abspath(location)
copy = {"copyLocation": copyFileLocation}
dataFile = open(copyData, "wb")
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mikemelch/hallie | hallie/modules/files.py | paste | def paste(location):
"""paste a file or directory that has been previously copied"""
copyData = settings.getDataFile()
if not location:
location = "."
try:
data = pickle.load(open(copyData, "rb"))
speech.speak("Pasting " + data["copyLocation"] + " to current directory.")
except:
speech.fail("It doesn't loo... | python | def paste(location):
"""paste a file or directory that has been previously copied"""
copyData = settings.getDataFile()
if not location:
location = "."
try:
data = pickle.load(open(copyData, "rb"))
speech.speak("Pasting " + data["copyLocation"] + " to current directory.")
except:
speech.fail("It doesn't loo... | [
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pyBookshelf/bookshelf | bookshelf/api_v2/pkg.py | add_zfs_apt_repository | def add_zfs_apt_repository():
""" adds the ZFS repository """
with settings(hide('warnings', 'running', 'stdout'),
warn_only=False, capture=True):
sudo('DEBIAN_FRONTEND=noninteractive /usr/bin/apt-get update')
install_ubuntu_development_tools()
apt_install(packages=['so... | python | def add_zfs_apt_repository():
""" adds the ZFS repository """
with settings(hide('warnings', 'running', 'stdout'),
warn_only=False, capture=True):
sudo('DEBIAN_FRONTEND=noninteractive /usr/bin/apt-get update')
install_ubuntu_development_tools()
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pyBookshelf/bookshelf | bookshelf/api_v2/pkg.py | apt_install | def apt_install(**kwargs):
"""
installs a apt package
"""
for pkg in list(kwargs['packages']):
if is_package_installed(distribution='ubuntu', pkg=pkg) is False:
sudo("DEBIAN_FRONTEND=noninteractive /usr/bin/apt-get install -y %s" % pkg)
# if we didn't abort above, we shou... | python | def apt_install(**kwargs):
"""
installs a apt package
"""
for pkg in list(kwargs['packages']):
if is_package_installed(distribution='ubuntu', pkg=pkg) is False:
sudo("DEBIAN_FRONTEND=noninteractive /usr/bin/apt-get install -y %s" % pkg)
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pyBookshelf/bookshelf | bookshelf/api_v2/pkg.py | apt_install_from_url | def apt_install_from_url(pkg_name, url, log=False):
""" installs a pkg from a url
p pkg_name: the name of the package to install
p url: the full URL for the rpm package
"""
if is_package_installed(distribution='ubuntu', pkg=pkg_name) is False:
if log:
log_green(
... | python | def apt_install_from_url(pkg_name, url, log=False):
""" installs a pkg from a url
p pkg_name: the name of the package to install
p url: the full URL for the rpm package
"""
if is_package_installed(distribution='ubuntu', pkg=pkg_name) is False:
if log:
log_green(
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pyBookshelf/bookshelf | bookshelf/api_v2/pkg.py | apt_add_key | def apt_add_key(keyid, keyserver='keyserver.ubuntu.com', log=False):
""" trust a new PGP key related to a apt-repository """
if log:
log_green(
'trusting keyid %s from %s' % (keyid, keyserver)
)
with settings(hide('warnings', 'running', 'stdout')):
sudo('apt-key adv --key... | python | def apt_add_key(keyid, keyserver='keyserver.ubuntu.com', log=False):
""" trust a new PGP key related to a apt-repository """
if log:
log_green(
'trusting keyid %s from %s' % (keyid, keyserver)
)
with settings(hide('warnings', 'running', 'stdout')):
sudo('apt-key adv --key... | [
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pyBookshelf/bookshelf | bookshelf/api_v2/pkg.py | enable_apt_repositories | def enable_apt_repositories(prefix, url, version, repositories):
""" adds an apt repository """
with settings(hide('warnings', 'running', 'stdout'),
warn_only=False, capture=True):
sudo('apt-add-repository "%s %s %s %s"' % (prefix,
url... | python | def enable_apt_repositories(prefix, url, version, repositories):
""" adds an apt repository """
with settings(hide('warnings', 'running', 'stdout'),
warn_only=False, capture=True):
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pyBookshelf/bookshelf | bookshelf/api_v2/pkg.py | install_python_module_locally | def install_python_module_locally(name):
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pyBookshelf/bookshelf | bookshelf/api_v2/pkg.py | is_package_installed | def is_package_installed(distribution, pkg):
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return(is_rpm_package_installed(pkg))
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""" checks if a particular package is installed """
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pyBookshelf/bookshelf | bookshelf/api_v2/pkg.py | is_rpm_package_installed | def is_rpm_package_installed(pkg):
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result = sudo("rpm -q %s" % pkg)
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pyBookshelf/bookshelf | bookshelf/api_v2/pkg.py | yum_install | def yum_install(**kwargs):
"""
installs a yum package
"""
if 'repo' in kwargs:
repo = kwargs['repo']
for pkg in list(kwargs['packages']):
if is_package_installed(distribution='el', pkg=pkg) is False:
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log_green(
... | python | def yum_install(**kwargs):
"""
installs a yum package
"""
if 'repo' in kwargs:
repo = kwargs['repo']
for pkg in list(kwargs['packages']):
if is_package_installed(distribution='el', pkg=pkg) is False:
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pyBookshelf/bookshelf | bookshelf/api_v2/pkg.py | yum_group_install | def yum_group_install(**kwargs):
""" instals a yum group """
for grp in list(kwargs['groups']):
log_green("installing %s ..." % grp)
if 'repo' in kwargs:
repo = kwargs['repo']
sudo("yum groupinstall -y --quiet "
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... | python | def yum_group_install(**kwargs):
""" instals a yum group """
for grp in list(kwargs['groups']):
log_green("installing %s ..." % grp)
if 'repo' in kwargs:
repo = kwargs['repo']
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pyBookshelf/bookshelf | bookshelf/api_v2/pkg.py | yum_install_from_url | def yum_install_from_url(pkg_name, url):
""" installs a pkg from a url
p pkg_name: the name of the package to install
p url: the full URL for the rpm package
"""
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log_green(
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""" installs a pkg from a url
p pkg_name: the name of the package to install
p url: the full URL for the rpm package
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benoitkugler/abstractDataLibrary | pyDLib/Core/controller.py | abstractInterface.recherche | def recherche(self, pattern, entete, in_all=False):
"""abstractSearch in fields of collection and reset rendering.
Returns number of results.
If in_all is True, call get_all before doing the search."""
if in_all:
self.collection = self.get_all()
self.collection.recher... | python | def recherche(self, pattern, entete, in_all=False):
"""abstractSearch in fields of collection and reset rendering.
Returns number of results.
If in_all is True, call get_all before doing the search."""
if in_all:
self.collection = self.get_all()
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benoitkugler/abstractDataLibrary | pyDLib/Core/controller.py | abstractInterface.launch_background_job | def launch_background_job(self, job, on_error=None, on_success=None):
"""Launch the callable job in background thread.
Succes or failure are controlled by on_error and on_success
"""
if not self.main.mode_online:
self.sortie_erreur_GUI(
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"""Launch the callable job in background thread.
Succes or failure are controlled by on_error and on_success
"""
if not self.main.mode_online:
self.sortie_erreur_GUI(
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benoitkugler/abstractDataLibrary | pyDLib/Core/controller.py | abstractInterface.filtre | def filtre(liste_base, criteres) -> groups.Collection:
"""
Return a filter list, bases on criteres
:param liste_base: Acces list
:param criteres: Criteria { `attribut`:[valeurs,...] }
"""
def choisi(ac):
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v = a... | python | def filtre(liste_base, criteres) -> groups.Collection:
"""
Return a filter list, bases on criteres
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:param criteres: Criteria { `attribut`:[valeurs,...] }
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def choisi(ac):
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benoitkugler/abstractDataLibrary | pyDLib/Core/controller.py | abstractInterInterfaces.load_remote_data | def load_remote_data(self, callback_etat=print):
"""
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On failure, raise :class:`~.Core.exceptions.StructureError`, :class:`~.Core.exceptions.ConnexionError`
:param callback_etat: State renderer str , int , int -> None
"""
callback_... | python | def load_remote_data(self, callback_etat=print):
"""
Load remote data. On succes, build base.
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benoitkugler/abstractDataLibrary | pyDLib/Core/controller.py | abstractInterInterfaces._load_users | def _load_users(self):
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Should setup `users` attribute"""
r = sql.abstractRequetesSQL.get_users()()
self.users = {d["id"]: dict(d) for d in r} | python | def _load_users(self):
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benoitkugler/abstractDataLibrary | pyDLib/Core/controller.py | abstractInterInterfaces.load_modules | def load_modules(self):
"""Should instance interfaces and set them to interface, following `modules`"""
if self.INTERFACES_MODULE is None:
raise NotImplementedError("A module containing interfaces modules "
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... | python | def load_modules(self):
"""Should instance interfaces and set them to interface, following `modules`"""
if self.INTERFACES_MODULE is None:
raise NotImplementedError("A module containing interfaces modules "
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benoitkugler/abstractDataLibrary | pyDLib/Core/controller.py | abstractInterInterfaces.has_autolog | def has_autolog(self, user_id):
"""
Read auto-connection parameters and returns local password or None
"""
try:
with open("local/init", "rb") as f:
s = f.read()
s = security.protege_data(s, False)
self.autolog = json.loads(s).ge... | python | def has_autolog(self, user_id):
"""
Read auto-connection parameters and returns local password or None
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benoitkugler/abstractDataLibrary | pyDLib/Core/controller.py | abstractInterInterfaces.loggin | def loggin(self, user_id, mdp, autolog):
"""Check mdp and return True it's ok"""
r = sql.abstractRequetesSQL.check_mdp_user(user_id, mdp)
if r():
# update auto-log params
self.autolog[user_id] = autolog and mdp or False
self.modules = self.users[user_id]["modu... | python | def loggin(self, user_id, mdp, autolog):
"""Check mdp and return True it's ok"""
r = sql.abstractRequetesSQL.check_mdp_user(user_id, mdp)
if r():
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OLC-Bioinformatics/sipprverse | cgecore/cmdline.py | cmd2list | def cmd2list(cmd):
''' Executes a command through the operating system and returns the output
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>>> from subprocess import Popen, PIPE
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stdout, ... | python | def cmd2list(cmd):
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OLC-Bioinformatics/sipprverse | pointfinder/PointFinder.py | find_mismatches | def find_mismatches(gene, sbjct_start, sbjct_seq, qry_seq, alternative_overlaps = []):
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OLC-Bioinformatics/sipprverse | pointfinder/PointFinder.py | find_nucleotid_mismatches | def find_nucleotid_mismatches(sbjct_start, sbjct_seq, qry_seq, promoter = False):
"""
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OLC-Bioinformatics/sipprverse | pointfinder/PointFinder.py | find_nuc_indel | def find_nuc_indel(gapped_seq, indel_seq):
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"""
ref_indel = indel_seq[0]
for j in range(1,len(gapped_seq)):
... | python | def find_nuc_indel(gapped_seq, indel_seq):
"""
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ref_indel = indel_seq[0]
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codon = codon.upper()
aa = {"ATT": "I", "ATC": "I", "ATA": "I",
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"""
This function converts a codon to an amino acid. If the codon is not
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"""
codon = codon.upper()
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OLC-Bioinformatics/sipprverse | pointfinder/PointFinder.py | get_codon | def get_codon(seq, codon_no, start_offset):
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"""
seq = seq.replace("-","")
codon_start_pos = int(codon_no - 1)*3 - start_offset
codon = seq[codon_start_pos:codon_start_pos + 3]
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"""
seq = seq.replace("-","")
codon_start_pos = int(codon_no - 1)*3 - start_offset
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OLC-Bioinformatics/sipprverse | pointfinder/PointFinder.py | name_insertion | def name_insertion(sbjct_seq, codon_no, sbjct_nucs, aa_alt, start_offset):
"""
This function is used to name a insertion mutation based on the HGVS
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"""
start_codon_no = codon_no - 1
if len(sbjct_nucs) == 3:
start_codon_no = codon_no
start_codon = get_codon(sbjct_seq... | python | def name_insertion(sbjct_seq, codon_no, sbjct_nucs, aa_alt, start_offset):
"""
This function is used to name a insertion mutation based on the HGVS
recommendation.
"""
start_codon_no = codon_no - 1
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OLC-Bioinformatics/sipprverse | pointfinder/PointFinder.py | name_indel_mutation | def name_indel_mutation(sbjct_seq, indel, sbjct_rf_indel, qry_rf_indel, codon_no, mut, start_offset):
"""
This function serves to name the individual mutations dependently on
the type of the mutation.
"""
# Get the subject and query sequences without gaps
sbjct_nucs = sbjct_rf_indel.replace("-"... | python | def name_indel_mutation(sbjct_seq, indel, sbjct_rf_indel, qry_rf_indel, codon_no, mut, start_offset):
"""
This function serves to name the individual mutations dependently on
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OLC-Bioinformatics/sipprverse | pointfinder/PointFinder.py | get_inframe_gap | def get_inframe_gap(seq, nucs_needed = 3):
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OLC-Bioinformatics/sipprverse | pointfinder/PointFinder.py | get_indels | def get_indels(sbjct_seq, qry_seq, start_pos):
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OLC-Bioinformatics/sipprverse | pointfinder/PointFinder.py | find_codon_mismatches | def find_codon_mismatches(sbjct_start, sbjct_seq, qry_seq):
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OLC-Bioinformatics/sipprverse | pointfinder/PointFinder.py | write_output | def write_output(gene, gene_name, mis_matches, known_mutations, known_stop_codon, unknown_flag, GENES):
"""
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pymacaron/pymacaron-core | pymacaron_core/swagger/apipool.py | ApiPool.merge | def merge(self):
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from one PyMacaron client stub to an other or when returning ... | python | def merge(self):
"""Try merging all the bravado_core models across all loaded APIs. If
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pymacaron/pymacaron-core | pymacaron_core/swagger/apipool.py | ApiPool._cmp_models | def _cmp_models(self, m1, m2):
"""Compare two models from different swagger APIs and tell if they are
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# Don't alter m1/m2 by mistake
m1 = copy.deepcopy(m1)
m2 = copy.deepcopy(m2)
# Remove keys added by bravado-core
def _... | python | def _cmp_models(self, m1, m2):
"""Compare two models from different swagger APIs and tell if they are
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# Don't alter m1/m2 by mistake
m1 = copy.deepcopy(m1)
m2 = copy.deepcopy(m2)
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saltant-org/saltant-py | saltant/models/base_task_type.py | BaseTaskType.sync | def sync(self):
"""Sync this model with latest data on the saltant server.
Note that in addition to returning the updated object, it also
updates the existing object.
Returns:
:class:`saltant.models.base_task_type.BaseTaskType`:
This task type instance after... | python | def sync(self):
"""Sync this model with latest data on the saltant server.
Note that in addition to returning the updated object, it also
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saltant-org/saltant-py | saltant/models/base_task_type.py | BaseTaskTypeManager.create | def create(
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name,
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description="",
environment_variables=None,
required_arguments=None,
required_arguments_default_values=None,
extra_data_to_post=None,
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"""Create a task type.
Args:
name (str): The n... | python | def create(
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command_to_run,
description="",
environment_variables=None,
required_arguments=None,
required_arguments_default_values=None,
extra_data_to_post=None,
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saltant-org/saltant-py | saltant/models/base_task_type.py | BaseTaskTypeManager.put | def put(
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Args:
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extra_data_to_put=None,
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saltant-org/saltant-py | saltant/models/base_task_type.py | BaseTaskTypeManager.response_data_to_model_instance | def response_data_to_model_instance(self, response_data):
"""Convert response data to a task type model.
Args:
response_data (dict): The data from the request's response.
Returns:
:class:`saltant.models.base_task_type.BaseTaskType`:
A model instance repr... | python | def response_data_to_model_instance(self, response_data):
"""Convert response data to a task type model.
Args:
response_data (dict): The data from the request's response.
Returns:
:class:`saltant.models.base_task_type.BaseTaskType`:
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crdoconnor/pathquery | hitch/key.py | regression | def regression():
"""
Run regression testing - lint and then run all tests.
"""
# HACK: Start using hitchbuildpy to get around this.
Command("touch", DIR.project.joinpath("pathquery", "__init__.py").abspath()).run()
storybook = _storybook({}).only_uninherited()
#storybook.with_params(**{"pyt... | python | def regression():
"""
Run regression testing - lint and then run all tests.
"""
# HACK: Start using hitchbuildpy to get around this.
Command("touch", DIR.project.joinpath("pathquery", "__init__.py").abspath()).run()
storybook = _storybook({}).only_uninherited()
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crdoconnor/pathquery | hitch/key.py | deploy | def deploy(version):
"""
Deploy to pypi as specified version.
"""
NAME = "pathquery"
git = Command("git").in_dir(DIR.project)
version_file = DIR.project.joinpath("VERSION")
old_version = version_file.bytes().decode('utf8')
if version_file.bytes().decode("utf8") != version:
DIR.pr... | python | def deploy(version):
"""
Deploy to pypi as specified version.
"""
NAME = "pathquery"
git = Command("git").in_dir(DIR.project)
version_file = DIR.project.joinpath("VERSION")
old_version = version_file.bytes().decode('utf8')
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crdoconnor/pathquery | hitch/key.py | hvenvup | def hvenvup(package, directory):
"""
Install a new version of a package in the hitch venv.
"""
pip = Command(DIR.gen.joinpath("hvenv", "bin", "pip"))
pip("uninstall", package, "-y").run()
pip("install", DIR.project.joinpath(directory).abspath()).run() | python | def hvenvup(package, directory):
"""
Install a new version of a package in the hitch venv.
"""
pip = Command(DIR.gen.joinpath("hvenv", "bin", "pip"))
pip("uninstall", package, "-y").run()
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crdoconnor/pathquery | hitch/key.py | Engine.set_up | def set_up(self):
"""Set up your applications and the test environment."""
self.path.state = self.path.gen.joinpath("state")
if self.path.state.exists():
self.path.state.rmtree(ignore_errors=True)
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... | python | def set_up(self):
"""Set up your applications and the test environment."""
self.path.state = self.path.gen.joinpath("state")
if self.path.state.exists():
self.path.state.rmtree(ignore_errors=True)
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beczkowb/csvparser | csvparser/parser.py | Parser.is_valid | def is_valid(self):
"""
Validates single instance. Returns boolean value and store errors in self.errors
"""
self.errors = []
for field in self.get_all_field_names_declared_by_user():
getattr(type(self), field).is_valid(self, type(self), field)
field_erro... | python | def is_valid(self):
"""
Validates single instance. Returns boolean value and store errors in self.errors
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OLC-Bioinformatics/sipprverse | method.py | Method.main | def main(self):
"""
Run the analyses using the inputted values for forward and reverse read length. However, if not all strains
pass the quality thresholds, continue to periodically run the analyses on these incomplete strains until either
all strains are complete, or the sequencing run ... | python | def main(self):
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