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fudge-py/fudge | fudge/__init__.py | Fake.without_args | def without_args(self, *args, **kwargs):
"""Set the last call to expect that certain arguments will not exist.
This is the opposite of :func:`fudge.Fake.with_matching_args`. It will
fail if any of the arguments are passed.
.. doctest::
>>> import fudge
>>> query = fudge.Fake('query').expects_call().without_args(
... 'http://example.com', name="Steve"
... )
>>> query('http://python.org', name="Joe")
>>> query('http://example.com')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with arg http://example.com
>>> query("Joe", "Frank", "Bartholomew", "Steve")
>>> query(name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query('http://python.org', name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query(city='Chicago', name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query.expects_call().without_args('http://example2.com')
fake:query
>>> query('foobar')
>>> query('foobar', 'http://example2.com')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with arg http://example2.com
>>> query.expects_call().without_args(name="Hieronymus")
fake:query
>>> query("Gottfried", "Hieronymus")
>>> query(name="Wexter", other_name="Hieronymus")
>>> query('asdf', name="Hieronymus")
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Hieronymus
>>> query(name="Hieronymus")
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Hieronymus
>>> query = fudge.Fake('query').expects_call().without_args(
... 'http://example.com', name="Steve"
... ).with_args('dog')
>>> query('dog')
>>> query('dog', 'http://example.com')
Traceback (most recent call last):
...
AssertionError: fake:query('dog') was called unexpectedly with args ('dog', 'http://example.com')
>>> query()
Traceback (most recent call last):
...
AssertionError: fake:query('dog') was called unexpectedly with args ()
"""
exp = self._get_current_call()
if args:
exp.unexpected_args = args
if kwargs:
exp.unexpected_kwargs = kwargs
return self | python | def without_args(self, *args, **kwargs):
"""Set the last call to expect that certain arguments will not exist.
This is the opposite of :func:`fudge.Fake.with_matching_args`. It will
fail if any of the arguments are passed.
.. doctest::
>>> import fudge
>>> query = fudge.Fake('query').expects_call().without_args(
... 'http://example.com', name="Steve"
... )
>>> query('http://python.org', name="Joe")
>>> query('http://example.com')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with arg http://example.com
>>> query("Joe", "Frank", "Bartholomew", "Steve")
>>> query(name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query('http://python.org', name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query(city='Chicago', name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query.expects_call().without_args('http://example2.com')
fake:query
>>> query('foobar')
>>> query('foobar', 'http://example2.com')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with arg http://example2.com
>>> query.expects_call().without_args(name="Hieronymus")
fake:query
>>> query("Gottfried", "Hieronymus")
>>> query(name="Wexter", other_name="Hieronymus")
>>> query('asdf', name="Hieronymus")
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Hieronymus
>>> query(name="Hieronymus")
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Hieronymus
>>> query = fudge.Fake('query').expects_call().without_args(
... 'http://example.com', name="Steve"
... ).with_args('dog')
>>> query('dog')
>>> query('dog', 'http://example.com')
Traceback (most recent call last):
...
AssertionError: fake:query('dog') was called unexpectedly with args ('dog', 'http://example.com')
>>> query()
Traceback (most recent call last):
...
AssertionError: fake:query('dog') was called unexpectedly with args ()
"""
exp = self._get_current_call()
if args:
exp.unexpected_args = args
if kwargs:
exp.unexpected_kwargs = kwargs
return self | [
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fail if any of the arguments are passed.
.. doctest::
>>> import fudge
>>> query = fudge.Fake('query').expects_call().without_args(
... 'http://example.com', name="Steve"
... )
>>> query('http://python.org', name="Joe")
>>> query('http://example.com')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with arg http://example.com
>>> query("Joe", "Frank", "Bartholomew", "Steve")
>>> query(name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query('http://python.org', name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query(city='Chicago', name='Steve')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Steve
>>> query.expects_call().without_args('http://example2.com')
fake:query
>>> query('foobar')
>>> query('foobar', 'http://example2.com')
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with arg http://example2.com
>>> query.expects_call().without_args(name="Hieronymus")
fake:query
>>> query("Gottfried", "Hieronymus")
>>> query(name="Wexter", other_name="Hieronymus")
>>> query('asdf', name="Hieronymus")
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Hieronymus
>>> query(name="Hieronymus")
Traceback (most recent call last):
...
AssertionError: fake:query() was called unexpectedly with kwarg name=Hieronymus
>>> query = fudge.Fake('query').expects_call().without_args(
... 'http://example.com', name="Steve"
... ).with_args('dog')
>>> query('dog')
>>> query('dog', 'http://example.com')
Traceback (most recent call last):
...
AssertionError: fake:query('dog') was called unexpectedly with args ('dog', 'http://example.com')
>>> query()
Traceback (most recent call last):
...
AssertionError: fake:query('dog') was called unexpectedly with args () | [
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fudge-py/fudge | fudge/__init__.py | Fake.with_arg_count | def with_arg_count(self, count):
"""Set the last call to expect an exact argument count.
I.E.::
>>> auth = Fake('auth').provides('login').with_arg_count(2)
>>> auth.login('joe_user') # forgot password
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called with 1 arg(s) but expected 2
"""
exp = self._get_current_call()
exp.expected_arg_count = count
return self | python | def with_arg_count(self, count):
"""Set the last call to expect an exact argument count.
I.E.::
>>> auth = Fake('auth').provides('login').with_arg_count(2)
>>> auth.login('joe_user') # forgot password
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called with 1 arg(s) but expected 2
"""
exp = self._get_current_call()
exp.expected_arg_count = count
return self | [
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>>> auth = Fake('auth').provides('login').with_arg_count(2)
>>> auth.login('joe_user') # forgot password
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called with 1 arg(s) but expected 2 | [
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fudge-py/fudge | fudge/__init__.py | Fake.with_kwarg_count | def with_kwarg_count(self, count):
"""Set the last call to expect an exact count of keyword arguments.
I.E.::
>>> auth = Fake('auth').provides('login').with_kwarg_count(2)
>>> auth.login(username='joe') # forgot password=
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called with 1 keyword arg(s) but expected 2
"""
exp = self._get_current_call()
exp.expected_kwarg_count = count
return self | python | def with_kwarg_count(self, count):
"""Set the last call to expect an exact count of keyword arguments.
I.E.::
>>> auth = Fake('auth').provides('login').with_kwarg_count(2)
>>> auth.login(username='joe') # forgot password=
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called with 1 keyword arg(s) but expected 2
"""
exp = self._get_current_call()
exp.expected_kwarg_count = count
return self | [
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>>> auth.login(username='joe') # forgot password=
Traceback (most recent call last):
...
AssertionError: fake:auth.login() was called with 1 keyword arg(s) but expected 2 | [
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thespacedoctor/sherlock | sherlock/database.py | database.connect | def connect(self):
"""connect to the various databases, the credientals and settings of which are found in the sherlock settings file
**Return:**
- ``transientsDbConn`` -- the database hosting the transient source data
- ``cataloguesDbConn`` -- connection to the database hosting the contextual catalogues the transients are to be crossmatched against
- ``pmDbConn`` -- connection to the PESSTO Marshall database
See the class docstring for usage
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``get`` method')
transientSettings = self.settings[
"database settings"]["transients"]
catalogueSettings = self.settings[
"database settings"]["static catalogues"]
if "pessto marshall" in self.settings[
"database settings"]:
marshallSettings = self.settings[
"database settings"]["pessto marshall"]
else:
marshallSettings = False
dbConns = []
for dbSettings in [transientSettings, catalogueSettings, marshallSettings]:
port = False
if dbSettings and dbSettings["tunnel"]:
port = self._setup_tunnel(
tunnelParameters=dbSettings["tunnel"]
)
if dbSettings:
# SETUP A DATABASE CONNECTION FOR THE STATIC CATALOGUES
host = dbSettings["host"]
user = dbSettings["user"]
passwd = dbSettings["password"]
dbName = dbSettings["db"]
thisConn = ms.connect(
host=host,
user=user,
passwd=passwd,
db=dbName,
port=port,
use_unicode=True,
charset='utf8',
client_flag=ms.constants.CLIENT.MULTI_STATEMENTS,
connect_timeout=3600
)
thisConn.autocommit(True)
dbConns.append(thisConn)
else:
dbConns.append(None)
# CREATE A DICTIONARY OF DATABASES
dbConns = {
"transients": dbConns[0],
"catalogues": dbConns[1],
"marshall": dbConns[2]
}
dbVersions = {}
for k, v in dbConns.iteritems():
if v:
sqlQuery = u"""
SELECT VERSION() as v;
""" % locals()
rows = readquery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=v,
quiet=False
)
version = rows[0]['v']
dbVersions[k] = version
else:
dbVersions[k] = None
self.log.debug('completed the ``get`` method')
return dbConns, dbVersions | python | def connect(self):
"""connect to the various databases, the credientals and settings of which are found in the sherlock settings file
**Return:**
- ``transientsDbConn`` -- the database hosting the transient source data
- ``cataloguesDbConn`` -- connection to the database hosting the contextual catalogues the transients are to be crossmatched against
- ``pmDbConn`` -- connection to the PESSTO Marshall database
See the class docstring for usage
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``get`` method')
transientSettings = self.settings[
"database settings"]["transients"]
catalogueSettings = self.settings[
"database settings"]["static catalogues"]
if "pessto marshall" in self.settings[
"database settings"]:
marshallSettings = self.settings[
"database settings"]["pessto marshall"]
else:
marshallSettings = False
dbConns = []
for dbSettings in [transientSettings, catalogueSettings, marshallSettings]:
port = False
if dbSettings and dbSettings["tunnel"]:
port = self._setup_tunnel(
tunnelParameters=dbSettings["tunnel"]
)
if dbSettings:
# SETUP A DATABASE CONNECTION FOR THE STATIC CATALOGUES
host = dbSettings["host"]
user = dbSettings["user"]
passwd = dbSettings["password"]
dbName = dbSettings["db"]
thisConn = ms.connect(
host=host,
user=user,
passwd=passwd,
db=dbName,
port=port,
use_unicode=True,
charset='utf8',
client_flag=ms.constants.CLIENT.MULTI_STATEMENTS,
connect_timeout=3600
)
thisConn.autocommit(True)
dbConns.append(thisConn)
else:
dbConns.append(None)
# CREATE A DICTIONARY OF DATABASES
dbConns = {
"transients": dbConns[0],
"catalogues": dbConns[1],
"marshall": dbConns[2]
}
dbVersions = {}
for k, v in dbConns.iteritems():
if v:
sqlQuery = u"""
SELECT VERSION() as v;
""" % locals()
rows = readquery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=v,
quiet=False
)
version = rows[0]['v']
dbVersions[k] = version
else:
dbVersions[k] = None
self.log.debug('completed the ``get`` method')
return dbConns, dbVersions | [
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**Return:**
- ``transientsDbConn`` -- the database hosting the transient source data
- ``cataloguesDbConn`` -- connection to the database hosting the contextual catalogues the transients are to be crossmatched against
- ``pmDbConn`` -- connection to the PESSTO Marshall database
See the class docstring for usage
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring | [
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thespacedoctor/sherlock | sherlock/database.py | database._setup_tunnel | def _setup_tunnel(
self,
tunnelParameters):
"""
*setup a ssh tunnel for a database connection to port through*
**Key Arguments:**
- ``tunnelParameters`` -- the tunnel parameters found associated with the database settings
**Return:**
- ``sshPort`` -- the port the ssh tunnel is connected via
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_setup_tunnel`` method')
# TEST TUNNEL DOES NOT ALREADY EXIST
sshPort = tunnelParameters["port"]
connected = self._checkServer(
"127.0.0.1", sshPort)
if connected:
self.log.debug('ssh tunnel already exists - moving on')
else:
# GRAB TUNNEL SETTINGS FROM SETTINGS FILE
ru = tunnelParameters["remote user"]
rip = tunnelParameters["remote ip"]
rh = tunnelParameters["remote datbase host"]
cmd = "ssh -fnN %(ru)s@%(rip)s -L %(sshPort)s:%(rh)s:3306" % locals()
p = Popen(cmd, shell=True, close_fds=True)
output = p.communicate()[0]
self.log.debug('output: %(output)s' % locals())
# TEST CONNECTION - QUIT AFTER SO MANY TRIES
connected = False
count = 0
while not connected:
connected = self._checkServer(
"127.0.0.1", sshPort)
time.sleep(1)
count += 1
if count == 5:
self.log.error(
'cound not setup tunnel to remote datbase' % locals())
sys.exit(0)
return sshPort | python | def _setup_tunnel(
self,
tunnelParameters):
"""
*setup a ssh tunnel for a database connection to port through*
**Key Arguments:**
- ``tunnelParameters`` -- the tunnel parameters found associated with the database settings
**Return:**
- ``sshPort`` -- the port the ssh tunnel is connected via
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_setup_tunnel`` method')
# TEST TUNNEL DOES NOT ALREADY EXIST
sshPort = tunnelParameters["port"]
connected = self._checkServer(
"127.0.0.1", sshPort)
if connected:
self.log.debug('ssh tunnel already exists - moving on')
else:
# GRAB TUNNEL SETTINGS FROM SETTINGS FILE
ru = tunnelParameters["remote user"]
rip = tunnelParameters["remote ip"]
rh = tunnelParameters["remote datbase host"]
cmd = "ssh -fnN %(ru)s@%(rip)s -L %(sshPort)s:%(rh)s:3306" % locals()
p = Popen(cmd, shell=True, close_fds=True)
output = p.communicate()[0]
self.log.debug('output: %(output)s' % locals())
# TEST CONNECTION - QUIT AFTER SO MANY TRIES
connected = False
count = 0
while not connected:
connected = self._checkServer(
"127.0.0.1", sshPort)
time.sleep(1)
count += 1
if count == 5:
self.log.error(
'cound not setup tunnel to remote datbase' % locals())
sys.exit(0)
return sshPort | [
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**Key Arguments:**
- ``tunnelParameters`` -- the tunnel parameters found associated with the database settings
**Return:**
- ``sshPort`` -- the port the ssh tunnel is connected via
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring | [
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thespacedoctor/sherlock | sherlock/database.py | database._checkServer | def _checkServer(self, address, port):
"""Check that the TCP Port we've decided to use for tunnelling is available
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_checkServer`` method')
# CREATE A TCP SOCKET
import socket
s = socket.socket()
self.log.debug(
"""Attempting to connect to `%(address)s` on port `%(port)s`""" % locals())
try:
s.connect((address, port))
self.log.debug(
"""Connected to `%(address)s` on port `%(port)s`""" % locals())
return True
except socket.error, e:
self.log.warning(
"""Connection to `%(address)s` on port `%(port)s` failed - try again: %(e)s""" % locals())
return False
return None | python | def _checkServer(self, address, port):
"""Check that the TCP Port we've decided to use for tunnelling is available
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_checkServer`` method')
# CREATE A TCP SOCKET
import socket
s = socket.socket()
self.log.debug(
"""Attempting to connect to `%(address)s` on port `%(port)s`""" % locals())
try:
s.connect((address, port))
self.log.debug(
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return True
except socket.error, e:
self.log.warning(
"""Connection to `%(address)s` on port `%(port)s` failed - try again: %(e)s""" % locals())
return False
return None | [
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- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring | [
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ozgurgunes/django-manifest | manifest/accounts/decorators.py | secure_required | def secure_required(view_func):
"""
Decorator to switch an url from http to https.
If a view is accessed through http and this decorator is applied
to that view, than it will return a permanent redirect to the
secure (https) version of the same view.
The decorator also must check that ``ACCOUNTS_USE_HTTPS`` is enabled.
If disabled, it should not redirect to https because the project
doesn't support it.
"""
def _wrapped_view(request, *args, **kwargs):
if not request.is_secure():
if defaults.ACCOUNTS_USE_HTTPS:
request_url = request.build_absolute_uri(
request.get_full_path())
secure_url = request_url.replace('http://', 'https://')
return HttpResponsePermanentRedirect(secure_url)
return view_func(request, *args, **kwargs)
return wraps(view_func,
assigned=available_attrs(view_func))(_wrapped_view) | python | def secure_required(view_func):
"""
Decorator to switch an url from http to https.
If a view is accessed through http and this decorator is applied
to that view, than it will return a permanent redirect to the
secure (https) version of the same view.
The decorator also must check that ``ACCOUNTS_USE_HTTPS`` is enabled.
If disabled, it should not redirect to https because the project
doesn't support it.
"""
def _wrapped_view(request, *args, **kwargs):
if not request.is_secure():
if defaults.ACCOUNTS_USE_HTTPS:
request_url = request.build_absolute_uri(
request.get_full_path())
secure_url = request_url.replace('http://', 'https://')
return HttpResponsePermanentRedirect(secure_url)
return view_func(request, *args, **kwargs)
return wraps(view_func,
assigned=available_attrs(view_func))(_wrapped_view) | [
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ozgurgunes/django-manifest | manifest/accounts/forms.py | identification_field_factory | def identification_field_factory(label, error_required):
"""
A simple identification field factory which enable you to set the label.
:param label:
String containing the label for this field.
:param error_required:
String containing the error message if the field is left empty.
"""
return forms.CharField(label=_(u"%(label)s") % {'label': label},
widget=forms.TextInput(attrs=attrs_dict),
max_length=75,
error_messages={'required': _(u"%(error)s") %
{'error': error_required}}) | python | def identification_field_factory(label, error_required):
"""
A simple identification field factory which enable you to set the label.
:param label:
String containing the label for this field.
:param error_required:
String containing the error message if the field is left empty.
"""
return forms.CharField(label=_(u"%(label)s") % {'label': label},
widget=forms.TextInput(attrs=attrs_dict),
max_length=75,
error_messages={'required': _(u"%(error)s") %
{'error': error_required}}) | [
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ozgurgunes/django-manifest | manifest/accounts/forms.py | RegistrationForm.clean_username | def clean_username(self):
"""
Validate that the username is unique and not listed
in ``defaults.ACCOUNTS_FORBIDDEN_USERNAMES`` list.
"""
try:
user = get_user_model().objects.get(username=self.cleaned_data["username"])
except get_user_model().DoesNotExist:
pass
else:
raise forms.ValidationError(
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if self.cleaned_data['username'].lower() \
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raise forms.ValidationError(_(u'This username is not allowed.'))
return self.cleaned_data['username'] | python | def clean_username(self):
"""
Validate that the username is unique and not listed
in ``defaults.ACCOUNTS_FORBIDDEN_USERNAMES`` list.
"""
try:
user = get_user_model().objects.get(username=self.cleaned_data["username"])
except get_user_model().DoesNotExist:
pass
else:
raise forms.ValidationError(
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if self.cleaned_data['username'].lower() \
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raise forms.ValidationError(_(u'This username is not allowed.'))
return self.cleaned_data['username'] | [
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ozgurgunes/django-manifest | manifest/accounts/forms.py | RegistrationForm.clean_email | def clean_email(self):
"""
Validate that the email address is unique.
"""
if get_user_model().objects.filter(
Q(email__iexact=self.cleaned_data['email']) |
Q(email_unconfirmed__iexact=self.cleaned_data['email'])):
raise forms.ValidationError(_(u'This email address is already '
'in use. Please supply a different email.'))
return self.cleaned_data['email'] | python | def clean_email(self):
"""
Validate that the email address is unique.
"""
if get_user_model().objects.filter(
Q(email__iexact=self.cleaned_data['email']) |
Q(email_unconfirmed__iexact=self.cleaned_data['email'])):
raise forms.ValidationError(_(u'This email address is already '
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return self.cleaned_data['email'] | [
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ozgurgunes/django-manifest | manifest/accounts/forms.py | RegistrationForm.save | def save(self):
"""
Creates a new user and account. Returns the newly created user.
"""
username, email, password = (self.cleaned_data['username'],
self.cleaned_data['email'],
self.cleaned_data['password1'])
user = get_user_model().objects.create_user(username, email, password,
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defaults.ACCOUNTS_ACTIVATION_REQUIRED)
return user | python | def save(self):
"""
Creates a new user and account. Returns the newly created user.
"""
username, email, password = (self.cleaned_data['username'],
self.cleaned_data['email'],
self.cleaned_data['password1'])
user = get_user_model().objects.create_user(username, email, password,
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defaults.ACCOUNTS_ACTIVATION_REQUIRED)
return user | [
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ozgurgunes/django-manifest | manifest/accounts/forms.py | AuthenticationForm.clean | def clean(self):
"""
Checks for the identification and password.
If the combination can't be found will raise an invalid sign in error.
"""
identification = self.cleaned_data.get('identification')
password = self.cleaned_data.get('password')
if identification and password:
self.user_cache = authenticate(identification=identification,
password=password)
if self.user_cache is None:
raise forms.ValidationError(_(u"Please enter a correct "
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return self.cleaned_data | python | def clean(self):
"""
Checks for the identification and password.
If the combination can't be found will raise an invalid sign in error.
"""
identification = self.cleaned_data.get('identification')
password = self.cleaned_data.get('password')
if identification and password:
self.user_cache = authenticate(identification=identification,
password=password)
if self.user_cache is None:
raise forms.ValidationError(_(u"Please enter a correct "
"username or email address and password. "
"Note that both fields are case-sensitive."))
return self.cleaned_data | [
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] | train | https://github.com/ozgurgunes/django-manifest/blob/9873bbf2a475b76284ad7e36b2b26c92131e72dd/manifest/accounts/forms.py#L181-L198 |
ozgurgunes/django-manifest | manifest/accounts/forms.py | EmailForm.clean_email | def clean_email(self):
"""
Validate that the email is not already registered with another user.
"""
if self.cleaned_data['email'].lower() == self.user.email:
raise forms.ValidationError(_(u"You're already known under "
"this email address."))
if get_user_model().objects.filter(
email__iexact=self.cleaned_data['email']).exclude(
email__iexact=self.user.email):
raise forms.ValidationError(_(u'This email address is already '
'in use. Please supply a different email address.'))
return self.cleaned_data['email'] | python | def clean_email(self):
"""
Validate that the email is not already registered with another user.
"""
if self.cleaned_data['email'].lower() == self.user.email:
raise forms.ValidationError(_(u"You're already known under "
"this email address."))
if get_user_model().objects.filter(
email__iexact=self.cleaned_data['email']).exclude(
email__iexact=self.user.email):
raise forms.ValidationError(_(u'This email address is already '
'in use. Please supply a different email address.'))
return self.cleaned_data['email'] | [
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ozgurgunes/django-manifest | manifest/accounts/forms.py | ProfileForm.clean_picture | def clean_picture(self):
"""
Validates format and file size of uploaded profile picture.
"""
if self.cleaned_data.get('picture'):
picture_data = self.cleaned_data['picture']
if 'error' in picture_data:
raise forms.ValidationError(_(u'Upload a valid image. '
'The file you uploaded was either not an image '
'or a corrupted image.'))
content_type = picture_data.content_type
if content_type:
main, sub = content_type.split('/')
if not (main == 'image'
and sub in defaults.ACCOUNTS_PICTURE_FORMATS):
raise forms.ValidationError(_(u'%s only.' %
defaults.ACCOUNTS_PICTURE_FORMATS))
if picture_data.size > int(defaults.ACCOUNTS_PICTURE_MAX_FILE):
raise forms.ValidationError(_(u'Image size is too big.'))
return self.cleaned_data['picture'] | python | def clean_picture(self):
"""
Validates format and file size of uploaded profile picture.
"""
if self.cleaned_data.get('picture'):
picture_data = self.cleaned_data['picture']
if 'error' in picture_data:
raise forms.ValidationError(_(u'Upload a valid image. '
'The file you uploaded was either not an image '
'or a corrupted image.'))
content_type = picture_data.content_type
if content_type:
main, sub = content_type.split('/')
if not (main == 'image'
and sub in defaults.ACCOUNTS_PICTURE_FORMATS):
raise forms.ValidationError(_(u'%s only.' %
defaults.ACCOUNTS_PICTURE_FORMATS))
if picture_data.size > int(defaults.ACCOUNTS_PICTURE_MAX_FILE):
raise forms.ValidationError(_(u'Image size is too big.'))
return self.cleaned_data['picture'] | [
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OpenEnergyPlatform/oedialect | oedialect/compiler.py | OECompiler.visit_grouping | def visit_grouping(self, grouping, asfrom=False, **kwargs):
""""
TODO:
"""
return {
'type': 'grouping',
'grouping': grouping.element._compiler_dispatch(self, **kwargs)
} | python | def visit_grouping(self, grouping, asfrom=False, **kwargs):
""""
TODO:
"""
return {
'type': 'grouping',
'grouping': grouping.element._compiler_dispatch(self, **kwargs)
} | [
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OpenEnergyPlatform/oedialect | oedialect/compiler.py | OECompiler.visit_select | def visit_select(self, select, asfrom=False, parens=True,
fromhints=None,
compound_index=0,
nested_join_translation=False,
select_wraps_for=None,
**kwargs):
jsn = {'command': 'advanced/search', 'type': 'select'}
needs_nested_translation = \
select.use_labels and \
not nested_join_translation and \
not self.stack and \
not self.dialect.supports_right_nested_joins
if needs_nested_translation:
transformed_select = self._transform_select_for_nested_joins(
select)
text = self.visit_select(
transformed_select, asfrom=asfrom, parens=parens,
fromhints=fromhints,
compound_index=compound_index,
nested_join_translation=True, **kwargs
)
toplevel = not self.stack
entry = self._default_stack_entry if toplevel else self.stack[-1]
populate_result_map = toplevel or \
(
compound_index == 0 and entry.get(
'need_result_map_for_compound', False)
) or entry.get('need_result_map_for_nested',
False)
# this was first proposed as part of #3372; however, it is not
# reached in current tests and could possibly be an assertion
# instead.
if not populate_result_map and 'add_to_result_map' in kwargs:
del kwargs['add_to_result_map']
if needs_nested_translation:
if populate_result_map:
self._transform_result_map_for_nested_joins(
select, transformed_select)
return jsn
froms = self._setup_select_stack(select, entry, asfrom)
column_clause_args = kwargs.copy()
column_clause_args.update({
'within_label_clause': False,
'within_columns_clause': False
})
if select._hints:
hint_text, byfrom = self._setup_select_hints(select)
if hint_text:
text += hint_text + " "
else:
byfrom = None
"""
if select._prefixes:
text += self._generate_prefixes(
select, select._prefixes, **kwargs)
"""
if select._distinct:
jsn['distinct'] = True
# the actual list of columns to print in the SELECT column list.
inner_columns = [
c for c in [
self._label_select_column(
select,
column,
populate_result_map, asfrom,
column_clause_args,
name=name)
for name, column in select._columns_plus_names
]
if c is not None
]
if populate_result_map and select_wraps_for is not None:
# if this select is a compiler-generated wrapper,
# rewrite the targeted columns in the result map
wrapped_inner_columns = set(select_wraps_for.inner_columns)
translate = dict(
(outer, inner.pop()) for outer, inner in [
(
outer,
outer.proxy_set.intersection(wrapped_inner_columns))
for outer in select.inner_columns
] if inner
)
self._result_columns = [
(key, name, tuple(translate.get(o, o) for o in obj), type_)
for key, name, obj, type_ in self._result_columns
]
jsn = self._compose_select_body(
jsn, select, inner_columns, froms, byfrom, kwargs)
if select._statement_hints:
per_dialect = [
ht for (dialect_name, ht)
in select._statement_hints
if dialect_name in ('*', self.dialect.name)
]
if per_dialect:
text += " " + self.get_statement_hint_text(per_dialect)
if self.ctes and self._is_toplevel_select(select):
text = self._render_cte_clause() + text
if select._suffixes:
text += " " + self._generate_prefixes(
select, select._suffixes, **kwargs)
self.stack.pop(-1)
if asfrom and parens:
return jsn # "(" + text + ")"
else:
return jsn | python | def visit_select(self, select, asfrom=False, parens=True,
fromhints=None,
compound_index=0,
nested_join_translation=False,
select_wraps_for=None,
**kwargs):
jsn = {'command': 'advanced/search', 'type': 'select'}
needs_nested_translation = \
select.use_labels and \
not nested_join_translation and \
not self.stack and \
not self.dialect.supports_right_nested_joins
if needs_nested_translation:
transformed_select = self._transform_select_for_nested_joins(
select)
text = self.visit_select(
transformed_select, asfrom=asfrom, parens=parens,
fromhints=fromhints,
compound_index=compound_index,
nested_join_translation=True, **kwargs
)
toplevel = not self.stack
entry = self._default_stack_entry if toplevel else self.stack[-1]
populate_result_map = toplevel or \
(
compound_index == 0 and entry.get(
'need_result_map_for_compound', False)
) or entry.get('need_result_map_for_nested',
False)
# this was first proposed as part of #3372; however, it is not
# reached in current tests and could possibly be an assertion
# instead.
if not populate_result_map and 'add_to_result_map' in kwargs:
del kwargs['add_to_result_map']
if needs_nested_translation:
if populate_result_map:
self._transform_result_map_for_nested_joins(
select, transformed_select)
return jsn
froms = self._setup_select_stack(select, entry, asfrom)
column_clause_args = kwargs.copy()
column_clause_args.update({
'within_label_clause': False,
'within_columns_clause': False
})
if select._hints:
hint_text, byfrom = self._setup_select_hints(select)
if hint_text:
text += hint_text + " "
else:
byfrom = None
"""
if select._prefixes:
text += self._generate_prefixes(
select, select._prefixes, **kwargs)
"""
if select._distinct:
jsn['distinct'] = True
# the actual list of columns to print in the SELECT column list.
inner_columns = [
c for c in [
self._label_select_column(
select,
column,
populate_result_map, asfrom,
column_clause_args,
name=name)
for name, column in select._columns_plus_names
]
if c is not None
]
if populate_result_map and select_wraps_for is not None:
# if this select is a compiler-generated wrapper,
# rewrite the targeted columns in the result map
wrapped_inner_columns = set(select_wraps_for.inner_columns)
translate = dict(
(outer, inner.pop()) for outer, inner in [
(
outer,
outer.proxy_set.intersection(wrapped_inner_columns))
for outer in select.inner_columns
] if inner
)
self._result_columns = [
(key, name, tuple(translate.get(o, o) for o in obj), type_)
for key, name, obj, type_ in self._result_columns
]
jsn = self._compose_select_body(
jsn, select, inner_columns, froms, byfrom, kwargs)
if select._statement_hints:
per_dialect = [
ht for (dialect_name, ht)
in select._statement_hints
if dialect_name in ('*', self.dialect.name)
]
if per_dialect:
text += " " + self.get_statement_hint_text(per_dialect)
if self.ctes and self._is_toplevel_select(select):
text = self._render_cte_clause() + text
if select._suffixes:
text += " " + self._generate_prefixes(
select, select._suffixes, **kwargs)
self.stack.pop(-1)
if asfrom and parens:
return jsn # "(" + text + ")"
else:
return jsn | [
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OpenEnergyPlatform/oedialect | oedialect/compiler.py | OECompiler._label_select_column | def _label_select_column(self, select, column,
populate_result_map,
asfrom, column_clause_args,
name=None,
within_columns_clause=True):
"""produce labeled columns present in a select()."""
if column.type._has_column_expression and \
populate_result_map:
col_expr = column.type.column_expression(column)
add_to_result_map = lambda keyname, name, objects, type_: \
self._add_to_result_map(
keyname, name,
(column,) + objects, type_)
else:
col_expr = column
if populate_result_map:
add_to_result_map = self._add_to_result_map
else:
add_to_result_map = None
if not within_columns_clause:
result_expr = col_expr
elif isinstance(column, elements.Label):
if col_expr is not column:
result_expr = compiler._CompileLabel(
col_expr,
column.name,
alt_names=(column.element,)
)
else:
result_expr = col_expr
elif select is not None and name:
result_expr = compiler._CompileLabel(
col_expr,
name,
alt_names=(column._key_label,)
)
elif \
asfrom and \
isinstance(column,
elements.ColumnClause) and \
not column.is_literal and \
column.table is not None and \
not isinstance(column.table, selectable.Select):
result_expr = compiler._CompileLabel(col_expr,
elements._as_truncated(
column.name),
alt_names=(column.key,))
elif (
not isinstance(column, elements.TextClause) and
(
not isinstance(column,
elements.UnaryExpression) or
column.wraps_column_expression
) and
(
not hasattr(column, 'name') or
isinstance(column, functions.Function)
)
):
result_expr = compiler._CompileLabel(col_expr, column.anon_label)
elif col_expr is not column:
# TODO: are we sure "column" has a .name and .key here ?
# assert isinstance(column, elements.ColumnClause)
result_expr = compiler._CompileLabel(col_expr,
elements._as_truncated(
column.name),
alt_names=(column.key,))
else:
result_expr = col_expr
column_clause_args.update(
within_columns_clause=within_columns_clause,
add_to_result_map=add_to_result_map
)
return result_expr._compiler_dispatch(
self,
**column_clause_args
) | python | def _label_select_column(self, select, column,
populate_result_map,
asfrom, column_clause_args,
name=None,
within_columns_clause=True):
"""produce labeled columns present in a select()."""
if column.type._has_column_expression and \
populate_result_map:
col_expr = column.type.column_expression(column)
add_to_result_map = lambda keyname, name, objects, type_: \
self._add_to_result_map(
keyname, name,
(column,) + objects, type_)
else:
col_expr = column
if populate_result_map:
add_to_result_map = self._add_to_result_map
else:
add_to_result_map = None
if not within_columns_clause:
result_expr = col_expr
elif isinstance(column, elements.Label):
if col_expr is not column:
result_expr = compiler._CompileLabel(
col_expr,
column.name,
alt_names=(column.element,)
)
else:
result_expr = col_expr
elif select is not None and name:
result_expr = compiler._CompileLabel(
col_expr,
name,
alt_names=(column._key_label,)
)
elif \
asfrom and \
isinstance(column,
elements.ColumnClause) and \
not column.is_literal and \
column.table is not None and \
not isinstance(column.table, selectable.Select):
result_expr = compiler._CompileLabel(col_expr,
elements._as_truncated(
column.name),
alt_names=(column.key,))
elif (
not isinstance(column, elements.TextClause) and
(
not isinstance(column,
elements.UnaryExpression) or
column.wraps_column_expression
) and
(
not hasattr(column, 'name') or
isinstance(column, functions.Function)
)
):
result_expr = compiler._CompileLabel(col_expr, column.anon_label)
elif col_expr is not column:
# TODO: are we sure "column" has a .name and .key here ?
# assert isinstance(column, elements.ColumnClause)
result_expr = compiler._CompileLabel(col_expr,
elements._as_truncated(
column.name),
alt_names=(column.key,))
else:
result_expr = col_expr
column_clause_args.update(
within_columns_clause=within_columns_clause,
add_to_result_map=add_to_result_map
)
return result_expr._compiler_dispatch(
self,
**column_clause_args
) | [
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pytroll/posttroll | posttroll/logger.py | run | def run():
"""Main function
"""
import argparse
global LOGGER
parser = argparse.ArgumentParser()
parser.add_argument("-r", "--rotated", help="Time rotated log file")
parser.add_argument("-v", "--verbose", help="print debug messages too",
action="store_true")
parser.add_argument("-s", "--server", help="server to listen to",
default="localhost")
parser.add_argument("-p", "--port", help="port to listen to",
default=16543,
type=int)
opts = parser.parse_args()
if opts.verbose:
loglevel = logging.DEBUG
else:
loglevel = logging.INFO
if opts.rotated:
handler = logging.handlers.TimedRotatingFileHandler(opts.rotated,
when="midnight",
backupCount=7)
else:
handler = logging.StreamHandler()
LOGGER = logging.getLogger("pytroll")
LOGGER.setLevel(loglevel)
handler.setLevel(loglevel)
formatter = ColoredFormatter("[%(asctime)s %(levelname)-19s] %(message)s")
handler.setFormatter(formatter)
LOGGER.addHandler(handler)
import time
try:
tlogger = Logger(opts.server, opts.port)
# logger = Logger("safe", 16543)
tlogger.start()
while True:
time.sleep(1)
except KeyboardInterrupt:
tlogger.stop()
print("Thanks for using pytroll/logger. "
"See you soon on www.pytroll.org!") | python | def run():
"""Main function
"""
import argparse
global LOGGER
parser = argparse.ArgumentParser()
parser.add_argument("-r", "--rotated", help="Time rotated log file")
parser.add_argument("-v", "--verbose", help="print debug messages too",
action="store_true")
parser.add_argument("-s", "--server", help="server to listen to",
default="localhost")
parser.add_argument("-p", "--port", help="port to listen to",
default=16543,
type=int)
opts = parser.parse_args()
if opts.verbose:
loglevel = logging.DEBUG
else:
loglevel = logging.INFO
if opts.rotated:
handler = logging.handlers.TimedRotatingFileHandler(opts.rotated,
when="midnight",
backupCount=7)
else:
handler = logging.StreamHandler()
LOGGER = logging.getLogger("pytroll")
LOGGER.setLevel(loglevel)
handler.setLevel(loglevel)
formatter = ColoredFormatter("[%(asctime)s %(levelname)-19s] %(message)s")
handler.setFormatter(formatter)
LOGGER.addHandler(handler)
import time
try:
tlogger = Logger(opts.server, opts.port)
# logger = Logger("safe", 16543)
tlogger.start()
while True:
time.sleep(1)
except KeyboardInterrupt:
tlogger.stop()
print("Thanks for using pytroll/logger. "
"See you soon on www.pytroll.org!") | [
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pytroll/posttroll | posttroll/logger.py | Logger.log | def log(self):
"""Log stuff.
"""
with Subscribe(services=[""], addr_listener=True) as sub:
for msg in sub.recv(1):
if msg:
if msg.type in ["log.debug", "log.info",
"log.warning", "log.error",
"log.critical"]:
getattr(LOGGER, msg.type[4:])(msg.subject + " " +
msg.sender + " " +
str(msg.data) + " " +
str(msg.time))
elif msg.binary:
LOGGER.debug("%s %s %s [binary] %s", msg.subject,
msg.sender,
msg.type,
str(msg.time))
else:
LOGGER.debug("%s %s %s %s %s", msg.subject,
msg.sender,
msg.type,
str(msg.data),
str(msg.time))
if not self.loop:
LOGGER.info("Stop logging")
break | python | def log(self):
"""Log stuff.
"""
with Subscribe(services=[""], addr_listener=True) as sub:
for msg in sub.recv(1):
if msg:
if msg.type in ["log.debug", "log.info",
"log.warning", "log.error",
"log.critical"]:
getattr(LOGGER, msg.type[4:])(msg.subject + " " +
msg.sender + " " +
str(msg.data) + " " +
str(msg.time))
elif msg.binary:
LOGGER.debug("%s %s %s [binary] %s", msg.subject,
msg.sender,
msg.type,
str(msg.time))
else:
LOGGER.debug("%s %s %s %s %s", msg.subject,
msg.sender,
msg.type,
str(msg.data),
str(msg.time))
if not self.loop:
LOGGER.info("Stop logging")
break | [
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emichael/PyREM | pyrem/task.py | cleanup | def cleanup():
"""Stop all started tasks on system exit.
Note: This only handles signals caught by the atexit module by default.
SIGKILL, for instance, will not be caught, so cleanup is not guaranteed in
all cases.
"""
to_stop = STARTED_TASKS.copy()
if to_stop:
print "Cleaning up..."
for task in to_stop:
try:
task.stop()
except: # pylint: disable=W0702
etype, value, trace = sys.exc_info()
# Disregard no such process exceptions, print out the rest
if not (isinstance(value, OSError) and value.errno == 3):
print ''.join(format_exception(etype, value, trace, None))
continue | python | def cleanup():
"""Stop all started tasks on system exit.
Note: This only handles signals caught by the atexit module by default.
SIGKILL, for instance, will not be caught, so cleanup is not guaranteed in
all cases.
"""
to_stop = STARTED_TASKS.copy()
if to_stop:
print "Cleaning up..."
for task in to_stop:
try:
task.stop()
except: # pylint: disable=W0702
etype, value, trace = sys.exc_info()
# Disregard no such process exceptions, print out the rest
if not (isinstance(value, OSError) and value.errno == 3):
print ''.join(format_exception(etype, value, trace, None))
continue | [
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emichael/PyREM | pyrem/task.py | Task.start | def start(self, wait=False):
"""Start a task.
This function depends on the underlying implementation of _start, which
any subclass of ``Task`` should implement.
Args:
wait (bool): Whether or not to wait on the task to finish before
returning from this function. Default `False`.
Raises:
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"""
if self._status is not TaskStatus.IDLE:
raise RuntimeError("Cannot start %s in state %s" %
(self, self._status))
self._status = TaskStatus.STARTED
STARTED_TASKS.add(self)
self._start()
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return self.return_values | python | def start(self, wait=False):
"""Start a task.
This function depends on the underlying implementation of _start, which
any subclass of ``Task`` should implement.
Args:
wait (bool): Whether or not to wait on the task to finish before
returning from this function. Default `False`.
Raises:
RuntimeError: If the task has already been started without a
subsequent call to ``reset()``.
"""
if self._status is not TaskStatus.IDLE:
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emichael/PyREM | pyrem/task.py | Task.wait | def wait(self):
"""Wait on a task to finish and stop it when it has finished.
Raises:
RuntimeError: If the task hasn't been started or has already been
stopped.
Returns:
The ``return_values`` of the task.
"""
if self._status is not TaskStatus.STARTED:
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return self.return_values | python | def wait(self):
"""Wait on a task to finish and stop it when it has finished.
Raises:
RuntimeError: If the task hasn't been started or has already been
stopped.
Returns:
The ``return_values`` of the task.
"""
if self._status is not TaskStatus.STARTED:
raise RuntimeError("Cannot wait on %s in state %s" %
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self._wait()
self.stop()
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emichael/PyREM | pyrem/task.py | Task.stop | def stop(self):
"""Stop a task immediately.
Raises:
RuntimeError: If the task hasn't been started or has already been
stopped.
"""
if self._status is TaskStatus.STOPPED:
return
if self._status is not TaskStatus.STARTED:
raise RuntimeError("Cannot stop %s in state %s" %
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self._stop()
STARTED_TASKS.remove(self)
self._status = TaskStatus.STOPPED | python | def stop(self):
"""Stop a task immediately.
Raises:
RuntimeError: If the task hasn't been started or has already been
stopped.
"""
if self._status is TaskStatus.STOPPED:
return
if self._status is not TaskStatus.STARTED:
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self._stop()
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emichael/PyREM | pyrem/task.py | Task.reset | def reset(self):
"""Reset a task.
Allows a task to be started again, clears the ``return_values``.
Raises:
RuntimeError: If the task has not been stopped.
"""
if self._status is not TaskStatus.STOPPED:
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self._reset()
self.return_values = {}
self._status = TaskStatus.IDLE | python | def reset(self):
"""Reset a task.
Allows a task to be started again, clears the ``return_values``.
Raises:
RuntimeError: If the task has not been stopped.
"""
if self._status is not TaskStatus.STOPPED:
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self._reset()
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emichael/PyREM | pyrem/task.py | Parallel._aggregate | def _aggregate(self):
"""Helper method to aggregate RemoteTasks into single ssh session."""
# pylint: disable=W0212
nonremote = [t for t in self._tasks if not isinstance(t, RemoteTask)]
remote = [t for t in self._tasks if isinstance(t, RemoteTask)]
host_dict = defaultdict(list)
for task in remote:
host_dict[task.host].append(task)
aggregated = []
for task_group in host_dict.values():
# Build up combined command
combined_cmd = []
for task in task_group:
if combined_cmd:
combined_cmd.append('&')
combined_cmd.append(' '.join(task._remote_command))
# Now, generated aggregate task
t0 = task_group[0] # pylint: disable=C0103
task = RemoteTask(
t0.host, combined_cmd, t0._quiet, t0._return_output,
t0._kill_remote, t0._identity_file)
aggregated.append(task)
self._tasks = nonremote + aggregated | python | def _aggregate(self):
"""Helper method to aggregate RemoteTasks into single ssh session."""
# pylint: disable=W0212
nonremote = [t for t in self._tasks if not isinstance(t, RemoteTask)]
remote = [t for t in self._tasks if isinstance(t, RemoteTask)]
host_dict = defaultdict(list)
for task in remote:
host_dict[task.host].append(task)
aggregated = []
for task_group in host_dict.values():
# Build up combined command
combined_cmd = []
for task in task_group:
if combined_cmd:
combined_cmd.append('&')
combined_cmd.append(' '.join(task._remote_command))
# Now, generated aggregate task
t0 = task_group[0] # pylint: disable=C0103
task = RemoteTask(
t0.host, combined_cmd, t0._quiet, t0._return_output,
t0._kill_remote, t0._identity_file)
aggregated.append(task)
self._tasks = nonremote + aggregated | [
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ozgurgunes/django-manifest | manifest/accounts/models.py | upload_to_picture | def upload_to_picture(instance, filename):
"""
Uploads a picture for a user to the ``ACCOUNTS_PICTURE_PATH`` and
saving it under unique hash for the image. This is for privacy
reasons so others can't just browse through the picture directory.
"""
extension = filename.split('.')[-1].lower()
salt, hash = generate_sha1(instance.id)
return '%(path)s/%(hash)s.%(extension)s' % {
'path': getattr(defaults,
'ACCOUNTS_PICTURE_PATH','%s/%s' % (
str(instance._meta.app_label),
str(instance._meta.model_name))),
'hash': hash[:10],
'extension': extension} | python | def upload_to_picture(instance, filename):
"""
Uploads a picture for a user to the ``ACCOUNTS_PICTURE_PATH`` and
saving it under unique hash for the image. This is for privacy
reasons so others can't just browse through the picture directory.
"""
extension = filename.split('.')[-1].lower()
salt, hash = generate_sha1(instance.id)
return '%(path)s/%(hash)s.%(extension)s' % {
'path': getattr(defaults,
'ACCOUNTS_PICTURE_PATH','%s/%s' % (
str(instance._meta.app_label),
str(instance._meta.model_name))),
'hash': hash[:10],
'extension': extension} | [
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ozgurgunes/django-manifest | manifest/accounts/models.py | AccountActivationMixin.activation_key_expired | def activation_key_expired(self):
"""
Checks if activation key is expired.
Returns ``True`` when the ``activation_key`` of the user is expired
and ``False`` if the key is still valid.
The key is expired when it's set to the value defined in
``ACCOUNTS_ACTIVATED`` or ``activation_key_created`` is beyond the
amount of days defined in ``ACCOUNTS_ACTIVATION_DAYS``.
"""
expiration_days = datetime.timedelta(
days=defaults.ACCOUNTS_ACTIVATION_DAYS)
expiration_date = self.date_joined + expiration_days
if self.activation_key == defaults.ACCOUNTS_ACTIVATED:
return True
if get_datetime_now() >= expiration_date:
return True
return False | python | def activation_key_expired(self):
"""
Checks if activation key is expired.
Returns ``True`` when the ``activation_key`` of the user is expired
and ``False`` if the key is still valid.
The key is expired when it's set to the value defined in
``ACCOUNTS_ACTIVATED`` or ``activation_key_created`` is beyond the
amount of days defined in ``ACCOUNTS_ACTIVATION_DAYS``.
"""
expiration_days = datetime.timedelta(
days=defaults.ACCOUNTS_ACTIVATION_DAYS)
expiration_date = self.date_joined + expiration_days
if self.activation_key == defaults.ACCOUNTS_ACTIVATED:
return True
if get_datetime_now() >= expiration_date:
return True
return False | [
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ozgurgunes/django-manifest | manifest/accounts/models.py | AccountActivationMixin.send_activation_email | def send_activation_email(self):
"""
Sends a activation email to the user.
This email is send when the user wants to activate their
newly created user.
"""
context= {'user': self,
'protocol': get_protocol(),
'activation_days': defaults.ACCOUNTS_ACTIVATION_DAYS,
'activation_key': self.activation_key,
'site': Site.objects.get_current()}
subject = ''.join(render_to_string(
'accounts/emails/activation_email_subject.txt',
context).splitlines())
message = render_to_string(
'accounts/emails/activation_email_message.txt',
context)
send_mail(subject,
message,
settings.DEFAULT_FROM_EMAIL,
[self.email,]) | python | def send_activation_email(self):
"""
Sends a activation email to the user.
This email is send when the user wants to activate their
newly created user.
"""
context= {'user': self,
'protocol': get_protocol(),
'activation_days': defaults.ACCOUNTS_ACTIVATION_DAYS,
'activation_key': self.activation_key,
'site': Site.objects.get_current()}
subject = ''.join(render_to_string(
'accounts/emails/activation_email_subject.txt',
context).splitlines())
message = render_to_string(
'accounts/emails/activation_email_message.txt',
context)
send_mail(subject,
message,
settings.DEFAULT_FROM_EMAIL,
[self.email,]) | [
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ozgurgunes/django-manifest | manifest/accounts/models.py | EmailConfirmationMixin.change_email | def change_email(self, email):
"""
Changes the email address for a user.
A user needs to verify this new email address before it becomes
active. By storing the new email address in a temporary field
-- ``temporary_email`` -- we are able to set this email address
after the user has verified it by clicking on the verification URI
in the email. This email gets send out by ``send_verification_email``.
:param email:
The new email address that the user wants to use.
"""
self.email_unconfirmed = email
salt, hash = generate_sha1(self.username)
self.email_confirmation_key = hash
self.email_confirmation_key_created = get_datetime_now()
self.save()
# Send email for activation
self.send_confirmation_email()
return self | python | def change_email(self, email):
"""
Changes the email address for a user.
A user needs to verify this new email address before it becomes
active. By storing the new email address in a temporary field
-- ``temporary_email`` -- we are able to set this email address
after the user has verified it by clicking on the verification URI
in the email. This email gets send out by ``send_verification_email``.
:param email:
The new email address that the user wants to use.
"""
self.email_unconfirmed = email
salt, hash = generate_sha1(self.username)
self.email_confirmation_key = hash
self.email_confirmation_key_created = get_datetime_now()
self.save()
# Send email for activation
self.send_confirmation_email()
return self | [
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ozgurgunes/django-manifest | manifest/accounts/models.py | EmailConfirmationMixin.send_confirmation_email | def send_confirmation_email(self):
"""
Sends an email to confirm the new email address.
This method sends out two emails. One to the new email address that
contains the ``email_confirmation_key`` which is used to verify this
this email address with :func:`User.objects.confirm_email`.
The other email is to the old email address to let the user know that
a request is made to change this email address.
"""
context= {'user': self,
'new_email': self.email_unconfirmed,
'protocol': get_protocol(),
'confirmation_key': self.email_confirmation_key,
'site': Site.objects.get_current()}
# Email to the old address
subject_old = ''.join(render_to_string(
'accounts/emails/confirmation_email_subject_old.txt',
context).splitlines())
message_old = render_to_string(
'accounts/emails/confirmation_email_message_old.txt',
context)
send_mail(subject_old,
message_old,
settings.DEFAULT_FROM_EMAIL,
[self.email])
# Email to the new address
subject_new = ''.join(render_to_string(
'accounts/emails/confirmation_email_subject_new.txt',
context).splitlines())
message_new = render_to_string(
'accounts/emails/confirmation_email_message_new.txt',
context)
send_mail(subject_new,
message_new,
settings.DEFAULT_FROM_EMAIL,
[self.email_unconfirmed,]) | python | def send_confirmation_email(self):
"""
Sends an email to confirm the new email address.
This method sends out two emails. One to the new email address that
contains the ``email_confirmation_key`` which is used to verify this
this email address with :func:`User.objects.confirm_email`.
The other email is to the old email address to let the user know that
a request is made to change this email address.
"""
context= {'user': self,
'new_email': self.email_unconfirmed,
'protocol': get_protocol(),
'confirmation_key': self.email_confirmation_key,
'site': Site.objects.get_current()}
# Email to the old address
subject_old = ''.join(render_to_string(
'accounts/emails/confirmation_email_subject_old.txt',
context).splitlines())
message_old = render_to_string(
'accounts/emails/confirmation_email_message_old.txt',
context)
send_mail(subject_old,
message_old,
settings.DEFAULT_FROM_EMAIL,
[self.email])
# Email to the new address
subject_new = ''.join(render_to_string(
'accounts/emails/confirmation_email_subject_new.txt',
context).splitlines())
message_new = render_to_string(
'accounts/emails/confirmation_email_message_new.txt',
context)
send_mail(subject_new,
message_new,
settings.DEFAULT_FROM_EMAIL,
[self.email_unconfirmed,]) | [
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ozgurgunes/django-manifest | manifest/accounts/models.py | UserProfileMixin.get_picture_url | def get_picture_url(self):
"""
Returns the image containing the picture for the user.
The picture can be a uploaded image or a Gravatar.
Gravatar functionality will only be used when
``ACCOUNTS_GRAVATAR_PICTURE`` is set to ``True``.
:return:
``None`` when Gravatar is not used and no default image is
supplied by ``ACCOUNTS_GRAVATAR_DEFAULT``.
"""
# First check for a picture and if any return that.
if self.picture:
return self.picture.url
# Use Gravatar if the user wants to.
if defaults.ACCOUNTS_GRAVATAR_PICTURE:
return get_gravatar(self.email,
defaults.ACCOUNTS_GRAVATAR_SIZE,
defaults.ACCOUNTS_GRAVATAR_DEFAULT)
# Gravatar not used, check for a default image.
else:
if defaults.ACCOUNTS_GRAVATAR_DEFAULT not in ['404', 'mm',
'identicon',
'monsterid',
'wavatar']:
return defaults.ACCOUNTS_GRAVATAR_DEFAULT
else: return None | python | def get_picture_url(self):
"""
Returns the image containing the picture for the user.
The picture can be a uploaded image or a Gravatar.
Gravatar functionality will only be used when
``ACCOUNTS_GRAVATAR_PICTURE`` is set to ``True``.
:return:
``None`` when Gravatar is not used and no default image is
supplied by ``ACCOUNTS_GRAVATAR_DEFAULT``.
"""
# First check for a picture and if any return that.
if self.picture:
return self.picture.url
# Use Gravatar if the user wants to.
if defaults.ACCOUNTS_GRAVATAR_PICTURE:
return get_gravatar(self.email,
defaults.ACCOUNTS_GRAVATAR_SIZE,
defaults.ACCOUNTS_GRAVATAR_DEFAULT)
# Gravatar not used, check for a default image.
else:
if defaults.ACCOUNTS_GRAVATAR_DEFAULT not in ['404', 'mm',
'identicon',
'monsterid',
'wavatar']:
return defaults.ACCOUNTS_GRAVATAR_DEFAULT
else: return None | [
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ozgurgunes/django-manifest | manifest/accounts/models.py | UserProfileMixin.get_full_name_or_username | def get_full_name_or_username(self):
"""
Returns the full name of the user, or if none is supplied will return
the username.
Also looks at ``ACCOUNTS_WITHOUT_USERNAMES`` settings to define if it
should return the username or email address when the full name is not
supplied.
:return:
``String`` containing the full name of the user. If no name is
supplied it will return the username or email address depending on
the ``ACCOUNTS_WITHOUT_USERNAMES`` setting.
"""
if self.first_name or self.last_name:
# We will return this as translated string. Maybe there are some
# countries that first display the last name.
name = _(u"%(first_name)s %(last_name)s") % \
{'first_name': self.first_name,
'last_name': self.last_name}
else:
# Fallback to the username if usernames are used
if not defaults.ACCOUNTS_WITHOUT_USERNAMES:
name = "%(username)s" % {'username': self.username}
else:
name = "%(email)s" % {'email': self.email}
return name.strip() | python | def get_full_name_or_username(self):
"""
Returns the full name of the user, or if none is supplied will return
the username.
Also looks at ``ACCOUNTS_WITHOUT_USERNAMES`` settings to define if it
should return the username or email address when the full name is not
supplied.
:return:
``String`` containing the full name of the user. If no name is
supplied it will return the username or email address depending on
the ``ACCOUNTS_WITHOUT_USERNAMES`` setting.
"""
if self.first_name or self.last_name:
# We will return this as translated string. Maybe there are some
# countries that first display the last name.
name = _(u"%(first_name)s %(last_name)s") % \
{'first_name': self.first_name,
'last_name': self.last_name}
else:
# Fallback to the username if usernames are used
if not defaults.ACCOUNTS_WITHOUT_USERNAMES:
name = "%(username)s" % {'username': self.username}
else:
name = "%(email)s" % {'email': self.email}
return name.strip() | [
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contentful-labs/contentful.py | contentful/cda/client.py | Client.validate_config | def validate_config(config):
"""Verify sanity for a :class:`.Config` instance.
This will raise an exception in case conditions are not met, otherwise
will complete silently.
:param config: (:class:`.Config`) Configuration container.
"""
non_null_params = ['space_id', 'access_token']
for param in non_null_params:
if getattr(config, param) is None:
raise Exception('Configuration for \"{0}\" must not be empty.'.format(param))
for clazz in config.custom_entries:
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raise Exception(
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elif clazz is Entry:
raise Exception('Cannot register "Entry" as a custom entry class.') | python | def validate_config(config):
"""Verify sanity for a :class:`.Config` instance.
This will raise an exception in case conditions are not met, otherwise
will complete silently.
:param config: (:class:`.Config`) Configuration container.
"""
non_null_params = ['space_id', 'access_token']
for param in non_null_params:
if getattr(config, param) is None:
raise Exception('Configuration for \"{0}\" must not be empty.'.format(param))
for clazz in config.custom_entries:
if not issubclass(clazz, Entry):
raise Exception(
'Provided class \"{0}\" must be a subclass of Entry.'.format(clazz.__name__))
elif clazz is Entry:
raise Exception('Cannot register "Entry" as a custom entry class.') | [
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contentful-labs/contentful.py | contentful/cda/client.py | Client.fetch | def fetch(self, resource_class):
"""Construct a :class:`.Request` for the given resource type.
Provided an :class:`.Entry` subclass, the Content Type ID will be inferred and requested explicitly.
Examples::
client.fetch(Asset)
client.fetch(Entry)
client.fetch(ContentType)
client.fetch(CustomEntryClass)
:param resource_class: The type of resource to be fetched.
:return: :class:`.Request` instance.
"""
if issubclass(resource_class, Entry):
params = None
content_type = getattr(resource_class, '__content_type__', None)
if content_type is not None:
params = {'content_type': resource_class.__content_type__}
return RequestArray(self.dispatcher, utils.path_for_class(resource_class), self.config.resolve_links,
params=params)
else:
remote_path = utils.path_for_class(resource_class)
if remote_path is None:
raise Exception('Invalid resource type \"{0}\".'.format(resource_class))
return RequestArray(self.dispatcher, remote_path, self.config.resolve_links) | python | def fetch(self, resource_class):
"""Construct a :class:`.Request` for the given resource type.
Provided an :class:`.Entry` subclass, the Content Type ID will be inferred and requested explicitly.
Examples::
client.fetch(Asset)
client.fetch(Entry)
client.fetch(ContentType)
client.fetch(CustomEntryClass)
:param resource_class: The type of resource to be fetched.
:return: :class:`.Request` instance.
"""
if issubclass(resource_class, Entry):
params = None
content_type = getattr(resource_class, '__content_type__', None)
if content_type is not None:
params = {'content_type': resource_class.__content_type__}
return RequestArray(self.dispatcher, utils.path_for_class(resource_class), self.config.resolve_links,
params=params)
else:
remote_path = utils.path_for_class(resource_class)
if remote_path is None:
raise Exception('Invalid resource type \"{0}\".'.format(resource_class))
return RequestArray(self.dispatcher, remote_path, self.config.resolve_links) | [
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contentful-labs/contentful.py | contentful/cda/client.py | Client.resolve | def resolve(self, link_resource_type, resource_id, array=None):
"""Resolve a link to a CDA resource.
Provided an `array` argument, attempt to retrieve the resource from the `mapped_items`
section of that array (containing both included and regular resources), in case the
resource cannot be found in the array (or if no `array` was provided) - attempt to fetch
the resource from the API by issuing a network request.
:param link_resource_type: (str) Resource type as str.
:param resource_id: (str) Remote ID of the linked resource.
:param array: (:class:`.Array`) Optional array resource.
:return: :class:`.Resource` subclass, `None` if it cannot be retrieved.
"""
result = None
if array is not None:
container = array.items_mapped.get(link_resource_type)
result = container.get(resource_id)
if result is None:
clz = utils.class_for_type(link_resource_type)
result = self.fetch(clz).where({'sys.id': resource_id}).first()
return result | python | def resolve(self, link_resource_type, resource_id, array=None):
"""Resolve a link to a CDA resource.
Provided an `array` argument, attempt to retrieve the resource from the `mapped_items`
section of that array (containing both included and regular resources), in case the
resource cannot be found in the array (or if no `array` was provided) - attempt to fetch
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:param link_resource_type: (str) Resource type as str.
:param resource_id: (str) Remote ID of the linked resource.
:param array: (:class:`.Array`) Optional array resource.
:return: :class:`.Resource` subclass, `None` if it cannot be retrieved.
"""
result = None
if array is not None:
container = array.items_mapped.get(link_resource_type)
result = container.get(resource_id)
if result is None:
clz = utils.class_for_type(link_resource_type)
result = self.fetch(clz).where({'sys.id': resource_id}).first()
return result | [
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contentful-labs/contentful.py | contentful/cda/client.py | Client.resolve_resource_link | def resolve_resource_link(self, resource_link, array=None):
"""Convenience method for resolving links given a :class:`.resources.ResourceLink` object.
Extract link values and pass to the :func:`.resolve` method of this class.
:param resource_link: (:class:`.ResourceLink`) instance.
:param array: (:class:`.Array`) Optional array resource.
:return: :class:`.Resource` subclass, `None` if it cannot be retrieved.
"""
return self.resolve(resource_link.link_type, resource_link.resource_id, array) | python | def resolve_resource_link(self, resource_link, array=None):
"""Convenience method for resolving links given a :class:`.resources.ResourceLink` object.
Extract link values and pass to the :func:`.resolve` method of this class.
:param resource_link: (:class:`.ResourceLink`) instance.
:param array: (:class:`.Array`) Optional array resource.
:return: :class:`.Resource` subclass, `None` if it cannot be retrieved.
"""
return self.resolve(resource_link.link_type, resource_link.resource_id, array) | [
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contentful-labs/contentful.py | contentful/cda/client.py | Client.resolve_dict_link | def resolve_dict_link(self, dct, array=None):
"""Convenience method for resolving links given a dict object.
Extract link values and pass to the :func:`.resolve` method of this class.
:param dct: (dict) Dictionary with the link data.
:param array: (:class:`.Array`) Optional array resource.
:return: :class:`.Resource` subclass, `None` if it cannot be retrieved.
"""
sys = dct.get('sys')
return self.resolve(sys['linkType'], sys['id'], array) if sys is not None else None | python | def resolve_dict_link(self, dct, array=None):
"""Convenience method for resolving links given a dict object.
Extract link values and pass to the :func:`.resolve` method of this class.
:param dct: (dict) Dictionary with the link data.
:param array: (:class:`.Array`) Optional array resource.
:return: :class:`.Resource` subclass, `None` if it cannot be retrieved.
"""
sys = dct.get('sys')
return self.resolve(sys['linkType'], sys['id'], array) if sys is not None else None | [
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contentful-labs/contentful.py | contentful/cda/client.py | Dispatcher.invoke | def invoke(self, request):
"""Invoke the given :class:`.Request` instance using the associated :class:`.Dispatcher`.
:param request: :class:`.Request` instance to invoke.
:return: :class:`.Resource` subclass.
"""
url = '{0}/{1}'.format(self.base_url, request.remote_path)
r = self.httpclient.get(url, params=request.params, headers=self.get_headers())
if 200 <= r.status_code < 300:
return self.resource_factory.from_json(r.json())
else:
if r.status_code in ErrorMapping.mapping:
raise ErrorMapping.mapping[r.status_code](r)
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raise ApiError(r) | python | def invoke(self, request):
"""Invoke the given :class:`.Request` instance using the associated :class:`.Dispatcher`.
:param request: :class:`.Request` instance to invoke.
:return: :class:`.Resource` subclass.
"""
url = '{0}/{1}'.format(self.base_url, request.remote_path)
r = self.httpclient.get(url, params=request.params, headers=self.get_headers())
if 200 <= r.status_code < 300:
return self.resource_factory.from_json(r.json())
else:
if r.status_code in ErrorMapping.mapping:
raise ErrorMapping.mapping[r.status_code](r)
else:
raise ApiError(r) | [
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contentful-labs/contentful.py | contentful/cda/client.py | RequestArray.all | def all(self):
"""Attempt to retrieve all available resources matching this request.
:return: Result instance as returned by the :class:`.Dispatcher`.
"""
result = self.invoke()
if self.resolve_links:
result.resolve_links()
return result | python | def all(self):
"""Attempt to retrieve all available resources matching this request.
:return: Result instance as returned by the :class:`.Dispatcher`.
"""
result = self.invoke()
if self.resolve_links:
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contentful-labs/contentful.py | contentful/cda/client.py | RequestArray.first | def first(self):
"""Attempt to retrieve only the first resource matching this request.
:return: Result instance, or `None` if there are no matching resources.
"""
self.params['limit'] = 1
result = self.all()
return result.items[0] if result.total > 0 else None | python | def first(self):
"""Attempt to retrieve only the first resource matching this request.
:return: Result instance, or `None` if there are no matching resources.
"""
self.params['limit'] = 1
result = self.all()
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contentful-labs/contentful.py | contentful/cda/client.py | RequestArray.where | def where(self, params):
"""Set a dict of parameters to be passed to the API when invoking this request.
:param params: (dict) query parameters.
:return: this :class:`.RequestArray` instance for convenience.
"""
self.params = dict(self.params, **params) # params overrides self.params
return self | python | def where(self, params):
"""Set a dict of parameters to be passed to the API when invoking this request.
:param params: (dict) query parameters.
:return: this :class:`.RequestArray` instance for convenience.
"""
self.params = dict(self.params, **params) # params overrides self.params
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dusktreader/py-buzz | examples/require_condition.py | complex_require_condition | def complex_require_condition():
"""
This function demonstrates a more complex usage of the require_condition
function. It shows argument interpolation and handling a more complex
boolean expression
"""
print("Demonstrating complex require_condition example")
val = 64
Buzz.require_condition(is_even(val), 'This condition should pass')
val = 81
Buzz.require_condition(is_even(val), 'Value {val} is not even', val=val) | python | def complex_require_condition():
"""
This function demonstrates a more complex usage of the require_condition
function. It shows argument interpolation and handling a more complex
boolean expression
"""
print("Demonstrating complex require_condition example")
val = 64
Buzz.require_condition(is_even(val), 'This condition should pass')
val = 81
Buzz.require_condition(is_even(val), 'Value {val} is not even', val=val) | [
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ozgurgunes/django-manifest | manifest/core/templatetags/navigation.py | active_url | def active_url(context, urls, css=None):
"""
Highlight menu item based on url tag.
Returns a css class if ``request.path`` is in given ``url``.
:param url:
Django url to be reversed.
:param css:
Css class to be returned for highlighting. Return active if none set.
"""
request = context['request']
if request.get_full_path in (reverse(url) for url in urls.split()):
return css if css else 'active'
return '' | python | def active_url(context, urls, css=None):
"""
Highlight menu item based on url tag.
Returns a css class if ``request.path`` is in given ``url``.
:param url:
Django url to be reversed.
:param css:
Css class to be returned for highlighting. Return active if none set.
"""
request = context['request']
if request.get_full_path in (reverse(url) for url in urls.split()):
return css if css else 'active'
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ozgurgunes/django-manifest | manifest/core/templatetags/navigation.py | active_path | def active_path(context, pattern, css=None):
"""
Highlight menu item based on path.
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:param pattern:
Regex url pattern.
:param css:
Css class to be returned for highlighting. Return active if none set.
"""
request = context['request']
#pattern = "^" + pattern + "$"
if re.search(pattern, request.path):
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"""
Highlight menu item based on path.
Returns a css class if ``request.path`` is in given ``pattern``.
:param pattern:
Regex url pattern.
:param css:
Css class to be returned for highlighting. Return active if none set.
"""
request = context['request']
#pattern = "^" + pattern + "$"
if re.search(pattern, request.path):
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zeroSteiner/smoke-zephyr | smoke_zephyr/configuration.py | MemoryConfiguration.get | def get(self, item_name):
"""
Retrieve the value of an option.
:param str item_name: The name of the option to retrieve.
:return: The value of *item_name* in the configuration.
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"""
Retrieve the value of an option.
:param str item_name: The name of the option to retrieve.
:return: The value of *item_name* in the configuration.
"""
if self.prefix:
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item_names = item_name.split(self.seperator)
node = self._storage
for item_name in item_names:
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zeroSteiner/smoke-zephyr | smoke_zephyr/configuration.py | MemoryConfiguration.get_if_exists | def get_if_exists(self, item_name, default_value=None):
"""
Retrieve the value of an option if it exists, otherwise
return *default_value* instead of raising an error:
:param str item_name: The name of the option to retrieve.
:param default_value: The value to return if *item_name* does not exist.
:return: The value of *item_name* in the configuration.
"""
if self.has_option(item_name):
return self.get(item_name)
return default_value | python | def get_if_exists(self, item_name, default_value=None):
"""
Retrieve the value of an option if it exists, otherwise
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:param str item_name: The name of the option to retrieve.
:param default_value: The value to return if *item_name* does not exist.
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zeroSteiner/smoke-zephyr | smoke_zephyr/configuration.py | MemoryConfiguration.has_option | def has_option(self, option_name):
"""
Check that an option exists.
:param str option_name: The name of the option to check.
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:rtype: bool
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"""
Check that an option exists.
:param str option_name: The name of the option to check.
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:rtype: bool
"""
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zeroSteiner/smoke-zephyr | smoke_zephyr/configuration.py | MemoryConfiguration.has_section | def has_section(self, section_name):
"""
Checks that an option exists and that it contains sub options.
:param str section_name: The name of the section to check.
:return: True if the section exists.
:rtype: dict
"""
if not self.has_option(section_name):
return False
return isinstance(self.get(section_name), dict) | python | def has_section(self, section_name):
"""
Checks that an option exists and that it contains sub options.
:param str section_name: The name of the section to check.
:return: True if the section exists.
:rtype: dict
"""
if not self.has_option(section_name):
return False
return isinstance(self.get(section_name), dict) | [
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zeroSteiner/smoke-zephyr | smoke_zephyr/configuration.py | MemoryConfiguration.set | def set(self, item_name, item_value):
"""
Sets the value of an option in the configuration.
:param str item_name: The name of the option to set.
:param item_value: The value of the option to set.
"""
if self.prefix:
item_name = self.prefix + self.seperator + item_name
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node = self._storage
for item_name in item_names:
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node = node[item_name]
node[item_last] = item_value
return | python | def set(self, item_name, item_value):
"""
Sets the value of an option in the configuration.
:param str item_name: The name of the option to set.
:param item_value: The value of the option to set.
"""
if self.prefix:
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node = self._storage
for item_name in item_names:
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node = node[item_name]
node[item_last] = item_value
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zeroSteiner/smoke-zephyr | smoke_zephyr/configuration.py | Configuration.get_missing | def get_missing(self, verify_file):
"""
Use a verification configuration which has a list of required options
and their respective types. This information is used to identify missing
and incompatible options in the loaded configuration.
:param str verify_file: The file to load for verification data.
:return: A dictionary of missing and incompatible settings.
:rtype: dict
"""
vconf = Configuration(verify_file)
missing = {}
for setting, setting_type in vconf.get('settings').items():
if not self.has_option(setting):
missing['missing'] = missing.get('settings', [])
missing['missing'].append(setting)
elif not type(self.get(setting)).__name__ == setting_type:
missing['incompatible'] = missing.get('incompatible', [])
missing['incompatible'].append((setting, setting_type))
return missing | python | def get_missing(self, verify_file):
"""
Use a verification configuration which has a list of required options
and their respective types. This information is used to identify missing
and incompatible options in the loaded configuration.
:param str verify_file: The file to load for verification data.
:return: A dictionary of missing and incompatible settings.
:rtype: dict
"""
vconf = Configuration(verify_file)
missing = {}
for setting, setting_type in vconf.get('settings').items():
if not self.has_option(setting):
missing['missing'] = missing.get('settings', [])
missing['missing'].append(setting)
elif not type(self.get(setting)).__name__ == setting_type:
missing['incompatible'] = missing.get('incompatible', [])
missing['incompatible'].append((setting, setting_type))
return missing | [
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zeroSteiner/smoke-zephyr | smoke_zephyr/configuration.py | Configuration.save | def save(self):
"""
Save the current configuration to disk.
"""
with open(self.configuration_file, 'w') as file_h:
file_h.write(self._serializer('dumps', self._storage)) | python | def save(self):
"""
Save the current configuration to disk.
"""
with open(self.configuration_file, 'w') as file_h:
file_h.write(self._serializer('dumps', self._storage)) | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | replace_lines | def replace_lines(regexer, handler, lines):
"""Uses replacement handler to perform replacements on lines of text
First we strip off all whitespace
We run the replacement on a clean 'content' string
Finally we replace the original content with the replaced version
This ensures that we retain the correct whitespace from the original line
"""
result = []
for line in lines:
content = line.strip()
replaced = regexer.sub(handler, content)
result.append(line.replace(content, replaced, 1))
return result | python | def replace_lines(regexer, handler, lines):
"""Uses replacement handler to perform replacements on lines of text
First we strip off all whitespace
We run the replacement on a clean 'content' string
Finally we replace the original content with the replaced version
This ensures that we retain the correct whitespace from the original line
"""
result = []
for line in lines:
content = line.strip()
replaced = regexer.sub(handler, content)
result.append(line.replace(content, replaced, 1))
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | write_targets | def write_targets(targets, **params):
"""Writes version info into version file"""
handler = ReplacementHandler(**params)
for target, regexer in regexer_for_targets(targets):
with open(target) as fh:
lines = fh.readlines()
lines = replace_lines(regexer, handler, lines)
with open(target, "w") as fh:
fh.writelines(lines)
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raise Exception(
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"""Writes version info into version file"""
handler = ReplacementHandler(**params)
for target, regexer in regexer_for_targets(targets):
with open(target) as fh:
lines = fh.readlines()
lines = replace_lines(regexer, handler, lines)
with open(target, "w") as fh:
fh.writelines(lines)
if handler.missing:
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | regexer_for_targets | def regexer_for_targets(targets):
"""Pairs up target files with their correct regex"""
for target in targets:
path, file_ext = os.path.splitext(target)
regexer = config.regexers[file_ext]
yield target, regexer | python | def regexer_for_targets(targets):
"""Pairs up target files with their correct regex"""
for target in targets:
path, file_ext = os.path.splitext(target)
regexer = config.regexers[file_ext]
yield target, regexer | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | extract_keypairs | def extract_keypairs(lines, regexer):
"""Given some lines of text, extract key-value pairs from them"""
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match = regexer.match(line.strip())
if not match:
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k_v = match.groupdict()
updates[k_v[Constants.KEY_GROUP]] = k_v[Constants.VALUE_GROUP]
return updates | python | def extract_keypairs(lines, regexer):
"""Given some lines of text, extract key-value pairs from them"""
updates = {}
for line in lines:
# for consistency we must match the replacer and strip whitespace / newlines
match = regexer.match(line.strip())
if not match:
continue
k_v = match.groupdict()
updates[k_v[Constants.KEY_GROUP]] = k_v[Constants.VALUE_GROUP]
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | read_targets | def read_targets(targets):
"""Reads generic key-value pairs from input files"""
results = {}
for target, regexer in regexer_for_targets(targets):
with open(target) as fh:
results.update(extract_keypairs(fh.readlines(), regexer))
return results | python | def read_targets(targets):
"""Reads generic key-value pairs from input files"""
results = {}
for target, regexer in regexer_for_targets(targets):
with open(target) as fh:
results.update(extract_keypairs(fh.readlines(), regexer))
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | detect_file_triggers | def detect_file_triggers(trigger_patterns):
"""The existence of files matching configured globs will trigger a version bump"""
triggers = set()
for trigger, pattern in trigger_patterns.items():
matches = glob.glob(pattern)
if matches:
_LOG.debug("trigger: %s bump from %r\n\t%s", trigger, pattern, matches)
triggers.add(trigger)
else:
_LOG.debug("trigger: no match on %r", pattern)
return triggers | python | def detect_file_triggers(trigger_patterns):
"""The existence of files matching configured globs will trigger a version bump"""
triggers = set()
for trigger, pattern in trigger_patterns.items():
matches = glob.glob(pattern)
if matches:
_LOG.debug("trigger: %s bump from %r\n\t%s", trigger, pattern, matches)
triggers.add(trigger)
else:
_LOG.debug("trigger: no match on %r", pattern)
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | get_all_triggers | def get_all_triggers(bump, file_triggers):
"""Aggregated set of significant figures to bump"""
triggers = set()
if file_triggers:
triggers = triggers.union(detect_file_triggers(config.trigger_patterns))
if bump:
_LOG.debug("trigger: %s bump requested", bump)
triggers.add(bump)
return triggers | python | def get_all_triggers(bump, file_triggers):
"""Aggregated set of significant figures to bump"""
triggers = set()
if file_triggers:
triggers = triggers.union(detect_file_triggers(config.trigger_patterns))
if bump:
_LOG.debug("trigger: %s bump requested", bump)
triggers.add(bump)
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | get_lock_behaviour | def get_lock_behaviour(triggers, all_data, lock):
"""Binary state lock protects from version increments if set"""
updates = {}
lock_key = config._forward_aliases.get(Constants.VERSION_LOCK_FIELD)
# if we are explicitly setting or locking the version, then set the lock field True anyway
if lock:
updates[Constants.VERSION_LOCK_FIELD] = config.VERSION_LOCK_VALUE
elif (
triggers
and lock_key
and str(all_data.get(lock_key)) == str(config.VERSION_LOCK_VALUE)
):
triggers.clear()
updates[Constants.VERSION_LOCK_FIELD] = config.VERSION_UNLOCK_VALUE
return updates | python | def get_lock_behaviour(triggers, all_data, lock):
"""Binary state lock protects from version increments if set"""
updates = {}
lock_key = config._forward_aliases.get(Constants.VERSION_LOCK_FIELD)
# if we are explicitly setting or locking the version, then set the lock field True anyway
if lock:
updates[Constants.VERSION_LOCK_FIELD] = config.VERSION_LOCK_VALUE
elif (
triggers
and lock_key
and str(all_data.get(lock_key)) == str(config.VERSION_LOCK_VALUE)
):
triggers.clear()
updates[Constants.VERSION_LOCK_FIELD] = config.VERSION_UNLOCK_VALUE
return updates | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | get_final_version_string | def get_final_version_string(release_mode, semver, commit_count=0):
"""Generates update dictionary entries for the version string"""
version_string = ".".join(semver)
maybe_dev_version_string = version_string
updates = {}
if release_mode:
# in production, we have something like `1.2.3`, as well as a flag e.g. PRODUCTION=True
updates[Constants.RELEASE_FIELD] = config.RELEASED_VALUE
else:
# in dev mode, we have a dev marker e.g. `1.2.3.dev678`
maybe_dev_version_string = config.DEVMODE_TEMPLATE.format(
version=version_string, count=commit_count
)
# make available all components of the semantic version including the full string
updates[Constants.VERSION_FIELD] = maybe_dev_version_string
updates[Constants.VERSION_STRICT_FIELD] = version_string
return updates | python | def get_final_version_string(release_mode, semver, commit_count=0):
"""Generates update dictionary entries for the version string"""
version_string = ".".join(semver)
maybe_dev_version_string = version_string
updates = {}
if release_mode:
# in production, we have something like `1.2.3`, as well as a flag e.g. PRODUCTION=True
updates[Constants.RELEASE_FIELD] = config.RELEASED_VALUE
else:
# in dev mode, we have a dev marker e.g. `1.2.3.dev678`
maybe_dev_version_string = config.DEVMODE_TEMPLATE.format(
version=version_string, count=commit_count
)
# make available all components of the semantic version including the full string
updates[Constants.VERSION_FIELD] = maybe_dev_version_string
updates[Constants.VERSION_STRICT_FIELD] = version_string
return updates | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | get_dvcs_info | def get_dvcs_info():
"""Gets current repository info from git"""
cmd = "git rev-list --count HEAD"
commit_count = str(
int(subprocess.check_output(shlex.split(cmd)).decode("utf8").strip())
)
cmd = "git rev-parse HEAD"
commit = str(subprocess.check_output(shlex.split(cmd)).decode("utf8").strip())
return {Constants.COMMIT_FIELD: commit, Constants.COMMIT_COUNT_FIELD: commit_count} | python | def get_dvcs_info():
"""Gets current repository info from git"""
cmd = "git rev-list --count HEAD"
commit_count = str(
int(subprocess.check_output(shlex.split(cmd)).decode("utf8").strip())
)
cmd = "git rev-parse HEAD"
commit = str(subprocess.check_output(shlex.split(cmd)).decode("utf8").strip())
return {Constants.COMMIT_FIELD: commit, Constants.COMMIT_COUNT_FIELD: commit_count} | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | main | def main(
set_to=None,
set_patch_count=None,
release=None,
bump=None,
lock=None,
file_triggers=None,
config_path=None,
**extra_updates
):
"""Main workflow.
Load config from cli and file
Detect "bump triggers" - things that cause a version increment
Find the current version
Create a new version
Write out new version and any other requested variables
:param set_to: explicitly set semver to this version string
:param set_patch_count: sets the patch number to the commit count
:param release: marks with a production flag
just sets a single flag as per config
:param bump: string indicating major/minor/patch
more significant bumps will zero the less significant ones
:param lock: locks the version string for the next call to autoversion
lock only removed if a version bump would have occurred
:param file_triggers: whether to enable bumping based on file triggers
bumping occurs once if any file(s) exist that match the config
:param config_path: path to config file
:param extra_updates:
:return:
"""
updates = {}
if config_path:
get_or_create_config(config_path, config)
for k, v in config.regexers.items():
config.regexers[k] = re.compile(v)
# a forward-mapping of the configured aliases
# giving <our config param> : <the configured value>
# if a value occurs multiple times, we take the last set value
for k, v in config.key_aliases.items():
config._forward_aliases[v] = k
all_data = read_targets(config.targets)
current_semver = semver.get_current_semver(all_data)
triggers = get_all_triggers(bump, file_triggers)
updates.update(get_lock_behaviour(triggers, all_data, lock))
updates.update(get_dvcs_info())
if set_to:
_LOG.debug("setting version directly: %s", set_to)
new_semver = auto_version.definitions.SemVer(*set_to.split("."))
if not lock:
warnings.warn(
"After setting version manually, does it need locking for a CI flow?",
UserWarning,
)
elif set_patch_count:
_LOG.debug(
"auto-incrementing version, using commit count for patch: %s",
updates[Constants.COMMIT_COUNT_FIELD],
)
new_semver = semver.make_new_semver(
current_semver, triggers, patch=updates[Constants.COMMIT_COUNT_FIELD]
)
else:
_LOG.debug("auto-incrementing version")
new_semver = semver.make_new_semver(current_semver, triggers)
updates.update(
get_final_version_string(
release_mode=release,
semver=new_semver,
commit_count=updates.get(Constants.COMMIT_COUNT_FIELD, 0),
)
)
for part in semver.SemVerSigFig:
updates[part] = getattr(new_semver, part)
# only rewrite a field that the user has specified in the configuration
native_updates = {
native: updates[key]
for native, key in config.key_aliases.items()
if key in updates
}
# finally, add in commandline overrides
native_updates.update(extra_updates)
write_targets(config.targets, **native_updates)
return current_semver, new_semver, native_updates | python | def main(
set_to=None,
set_patch_count=None,
release=None,
bump=None,
lock=None,
file_triggers=None,
config_path=None,
**extra_updates
):
"""Main workflow.
Load config from cli and file
Detect "bump triggers" - things that cause a version increment
Find the current version
Create a new version
Write out new version and any other requested variables
:param set_to: explicitly set semver to this version string
:param set_patch_count: sets the patch number to the commit count
:param release: marks with a production flag
just sets a single flag as per config
:param bump: string indicating major/minor/patch
more significant bumps will zero the less significant ones
:param lock: locks the version string for the next call to autoversion
lock only removed if a version bump would have occurred
:param file_triggers: whether to enable bumping based on file triggers
bumping occurs once if any file(s) exist that match the config
:param config_path: path to config file
:param extra_updates:
:return:
"""
updates = {}
if config_path:
get_or_create_config(config_path, config)
for k, v in config.regexers.items():
config.regexers[k] = re.compile(v)
# a forward-mapping of the configured aliases
# giving <our config param> : <the configured value>
# if a value occurs multiple times, we take the last set value
for k, v in config.key_aliases.items():
config._forward_aliases[v] = k
all_data = read_targets(config.targets)
current_semver = semver.get_current_semver(all_data)
triggers = get_all_triggers(bump, file_triggers)
updates.update(get_lock_behaviour(triggers, all_data, lock))
updates.update(get_dvcs_info())
if set_to:
_LOG.debug("setting version directly: %s", set_to)
new_semver = auto_version.definitions.SemVer(*set_to.split("."))
if not lock:
warnings.warn(
"After setting version manually, does it need locking for a CI flow?",
UserWarning,
)
elif set_patch_count:
_LOG.debug(
"auto-incrementing version, using commit count for patch: %s",
updates[Constants.COMMIT_COUNT_FIELD],
)
new_semver = semver.make_new_semver(
current_semver, triggers, patch=updates[Constants.COMMIT_COUNT_FIELD]
)
else:
_LOG.debug("auto-incrementing version")
new_semver = semver.make_new_semver(current_semver, triggers)
updates.update(
get_final_version_string(
release_mode=release,
semver=new_semver,
commit_count=updates.get(Constants.COMMIT_COUNT_FIELD, 0),
)
)
for part in semver.SemVerSigFig:
updates[part] = getattr(new_semver, part)
# only rewrite a field that the user has specified in the configuration
native_updates = {
native: updates[key]
for native, key in config.key_aliases.items()
if key in updates
}
# finally, add in commandline overrides
native_updates.update(extra_updates)
write_targets(config.targets, **native_updates)
return current_semver, new_semver, native_updates | [
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Create a new version
Write out new version and any other requested variables
:param set_to: explicitly set semver to this version string
:param set_patch_count: sets the patch number to the commit count
:param release: marks with a production flag
just sets a single flag as per config
:param bump: string indicating major/minor/patch
more significant bumps will zero the less significant ones
:param lock: locks the version string for the next call to autoversion
lock only removed if a version bump would have occurred
:param file_triggers: whether to enable bumping based on file triggers
bumping occurs once if any file(s) exist that match the config
:param config_path: path to config file
:param extra_updates:
:return: | [
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ARMmbed/autoversion | src/auto_version/auto_version_tool.py | main_from_cli | def main_from_cli():
"""Main workflow.
Load config from cli and file
Detect "bump triggers" - things that cause a version increment
Find the current version
Create a new version
Write out new version and any other requested variables
"""
args, others = get_cli()
if args.version:
print(__version__)
exit(0)
log_level = logging.WARNING - 10 * args.verbosity
logging.basicConfig(level=log_level, format="%(module)s %(levelname)8s %(message)s")
command_line_updates = parse_other_args(others)
old, new, updates = main(
set_to=args.set,
set_patch_count=args.set_patch_count,
lock=args.lock,
release=args.release,
bump=args.bump,
file_triggers=args.file_triggers,
config_path=args.config,
**command_line_updates
)
_LOG.info("previously: %s", old)
_LOG.info("currently: %s", new)
_LOG.debug("updates:\n%s", pprint.pformat(updates))
print(
updates.get(config._forward_aliases.get(Constants.VERSION_FIELD))
or updates.get(config._forward_aliases.get(Constants.VERSION_STRICT_FIELD))
) | python | def main_from_cli():
"""Main workflow.
Load config from cli and file
Detect "bump triggers" - things that cause a version increment
Find the current version
Create a new version
Write out new version and any other requested variables
"""
args, others = get_cli()
if args.version:
print(__version__)
exit(0)
log_level = logging.WARNING - 10 * args.verbosity
logging.basicConfig(level=log_level, format="%(module)s %(levelname)8s %(message)s")
command_line_updates = parse_other_args(others)
old, new, updates = main(
set_to=args.set,
set_patch_count=args.set_patch_count,
lock=args.lock,
release=args.release,
bump=args.bump,
file_triggers=args.file_triggers,
config_path=args.config,
**command_line_updates
)
_LOG.info("previously: %s", old)
_LOG.info("currently: %s", new)
_LOG.debug("updates:\n%s", pprint.pformat(updates))
print(
updates.get(config._forward_aliases.get(Constants.VERSION_FIELD))
or updates.get(config._forward_aliases.get(Constants.VERSION_STRICT_FIELD))
) | [
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Load config from cli and file
Detect "bump triggers" - things that cause a version increment
Find the current version
Create a new version
Write out new version and any other requested variables | [
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] | train | https://github.com/ARMmbed/autoversion/blob/c5b127d2059c8219f5637fe45bf9e1be3a0af2aa/src/auto_version/auto_version_tool.py#L284-L320 |
Clinical-Genomics/trailblazer | trailblazer/cli/core.py | log_cmd | def log_cmd(context, sampleinfo, sacct, quiet, config):
"""Log an analysis.
CONFIG: MIP config file for an analysis
"""
log_analysis = LogAnalysis(context.obj['store'])
try:
new_run = log_analysis(config, sampleinfo=sampleinfo, sacct=sacct)
except MissingFileError as error:
click.echo(click.style(f"Skipping, missing Sacct file: {error.message}", fg='yellow'))
return
except KeyError as error:
print(click.style(f"unexpected output, missing key: {error.args[0]}", fg='yellow'))
return
if new_run is None:
if not quiet:
click.echo(click.style('Analysis already logged', fg='yellow'))
else:
message = f"New log added: {new_run.family} ({new_run.id}) - {new_run.status}"
click.echo(click.style(message, fg='green')) | python | def log_cmd(context, sampleinfo, sacct, quiet, config):
"""Log an analysis.
CONFIG: MIP config file for an analysis
"""
log_analysis = LogAnalysis(context.obj['store'])
try:
new_run = log_analysis(config, sampleinfo=sampleinfo, sacct=sacct)
except MissingFileError as error:
click.echo(click.style(f"Skipping, missing Sacct file: {error.message}", fg='yellow'))
return
except KeyError as error:
print(click.style(f"unexpected output, missing key: {error.args[0]}", fg='yellow'))
return
if new_run is None:
if not quiet:
click.echo(click.style('Analysis already logged', fg='yellow'))
else:
message = f"New log added: {new_run.family} ({new_run.id}) - {new_run.status}"
click.echo(click.style(message, fg='green')) | [
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] | train | https://github.com/Clinical-Genomics/trailblazer/blob/27f3cd21043a1077bd7029e85783459a50a7b798/trailblazer/cli/core.py#L49-L68 |
Clinical-Genomics/trailblazer | trailblazer/cli/core.py | start | def start(context, mip_config, email, priority, dryrun, command, start_with, family):
"""Start a new analysis."""
mip_cli = MipCli(context.obj['script'])
mip_config = mip_config or context.obj['mip_config']
email = email or environ_email()
kwargs = dict(config=mip_config, family=family, priority=priority, email=email, dryrun=dryrun, start_with=start_with)
if command:
mip_command = mip_cli.build_command(**kwargs)
click.echo(' '.join(mip_command))
else:
try:
mip_cli(**kwargs)
if not dryrun:
context.obj['store'].add_pending(family, email=email)
except MipStartError as error:
click.echo(click.style(error.message, fg='red')) | python | def start(context, mip_config, email, priority, dryrun, command, start_with, family):
"""Start a new analysis."""
mip_cli = MipCli(context.obj['script'])
mip_config = mip_config or context.obj['mip_config']
email = email or environ_email()
kwargs = dict(config=mip_config, family=family, priority=priority, email=email, dryrun=dryrun, start_with=start_with)
if command:
mip_command = mip_cli.build_command(**kwargs)
click.echo(' '.join(mip_command))
else:
try:
mip_cli(**kwargs)
if not dryrun:
context.obj['store'].add_pending(family, email=email)
except MipStartError as error:
click.echo(click.style(error.message, fg='red')) | [
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Clinical-Genomics/trailblazer | trailblazer/cli/core.py | init | def init(context, reset, force):
"""Setup the database."""
existing_tables = context.obj['store'].engine.table_names()
if force or reset:
if existing_tables and not force:
message = f"Delete existing tables? [{', '.join(existing_tables)}]"
click.confirm(click.style(message, fg='yellow'), abort=True)
context.obj['store'].drop_all()
elif existing_tables:
click.echo(click.style("Database already exists, use '--reset'", fg='red'))
context.abort()
context.obj['store'].setup()
message = f"Success! New tables: {', '.join(context.obj['store'].engine.table_names())}"
click.echo(click.style(message, fg='green')) | python | def init(context, reset, force):
"""Setup the database."""
existing_tables = context.obj['store'].engine.table_names()
if force or reset:
if existing_tables and not force:
message = f"Delete existing tables? [{', '.join(existing_tables)}]"
click.confirm(click.style(message, fg='yellow'), abort=True)
context.obj['store'].drop_all()
elif existing_tables:
click.echo(click.style("Database already exists, use '--reset'", fg='red'))
context.abort()
context.obj['store'].setup()
message = f"Success! New tables: {', '.join(context.obj['store'].engine.table_names())}"
click.echo(click.style(message, fg='green')) | [
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Clinical-Genomics/trailblazer | trailblazer/cli/core.py | scan | def scan(context, root_dir):
"""Scan a directory for analyses."""
root_dir = root_dir or context.obj['root']
config_files = Path(root_dir).glob('*/analysis/*_config.yaml')
for config_file in config_files:
LOG.debug("found analysis config: %s", config_file)
with config_file.open() as stream:
context.invoke(log_cmd, config=stream, quiet=True)
context.obj['store'].track_update() | python | def scan(context, root_dir):
"""Scan a directory for analyses."""
root_dir = root_dir or context.obj['root']
config_files = Path(root_dir).glob('*/analysis/*_config.yaml')
for config_file in config_files:
LOG.debug("found analysis config: %s", config_file)
with config_file.open() as stream:
context.invoke(log_cmd, config=stream, quiet=True)
context.obj['store'].track_update() | [
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] | train | https://github.com/Clinical-Genomics/trailblazer/blob/27f3cd21043a1077bd7029e85783459a50a7b798/trailblazer/cli/core.py#L122-L131 |
Clinical-Genomics/trailblazer | trailblazer/cli/core.py | user | def user(context, name, email):
"""Add a new or display information about an existing user."""
existing_user = context.obj['store'].user(email)
if existing_user:
click.echo(existing_user.to_dict())
elif name:
new_user = context.obj['store'].add_user(name, email)
click.echo(click.style(f"New user added: {email} ({new_user.id})", fg='green'))
else:
click.echo(click.style('User not found', fg='yellow')) | python | def user(context, name, email):
"""Add a new or display information about an existing user."""
existing_user = context.obj['store'].user(email)
if existing_user:
click.echo(existing_user.to_dict())
elif name:
new_user = context.obj['store'].add_user(name, email)
click.echo(click.style(f"New user added: {email} ({new_user.id})", fg='green'))
else:
click.echo(click.style('User not found', fg='yellow')) | [
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Clinical-Genomics/trailblazer | trailblazer/cli/core.py | cancel | def cancel(context, jobs, analysis_id):
"""Cancel all jobs in a run."""
analysis_obj = context.obj['store'].analysis(analysis_id)
if analysis_obj is None:
click.echo('analysis not found')
context.abort()
elif analysis_obj.status != 'running':
click.echo(f"analysis not running: {analysis_obj.status}")
context.abort()
config_path = Path(analysis_obj.config_path)
with config_path.open() as config_stream:
config_raw = ruamel.yaml.safe_load(config_stream)
config_data = parse_config(config_raw)
log_path = Path(f"{config_data['log_path']}")
if not log_path.exists():
click.echo(f"missing MIP log file: {log_path}")
context.abort()
with log_path.open() as log_stream:
all_jobs = job_ids(log_stream)
if jobs:
for job_id in all_jobs:
click.echo(job_id)
else:
for job_id in all_jobs:
LOG.debug(f"cancelling job: {job_id}")
process = subprocess.Popen(['scancel', job_id])
process.wait()
analysis_obj.status = 'canceled'
context.obj['store'].commit()
click.echo('cancelled analysis successfully!') | python | def cancel(context, jobs, analysis_id):
"""Cancel all jobs in a run."""
analysis_obj = context.obj['store'].analysis(analysis_id)
if analysis_obj is None:
click.echo('analysis not found')
context.abort()
elif analysis_obj.status != 'running':
click.echo(f"analysis not running: {analysis_obj.status}")
context.abort()
config_path = Path(analysis_obj.config_path)
with config_path.open() as config_stream:
config_raw = ruamel.yaml.safe_load(config_stream)
config_data = parse_config(config_raw)
log_path = Path(f"{config_data['log_path']}")
if not log_path.exists():
click.echo(f"missing MIP log file: {log_path}")
context.abort()
with log_path.open() as log_stream:
all_jobs = job_ids(log_stream)
if jobs:
for job_id in all_jobs:
click.echo(job_id)
else:
for job_id in all_jobs:
LOG.debug(f"cancelling job: {job_id}")
process = subprocess.Popen(['scancel', job_id])
process.wait()
analysis_obj.status = 'canceled'
context.obj['store'].commit()
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] | train | https://github.com/Clinical-Genomics/trailblazer/blob/27f3cd21043a1077bd7029e85783459a50a7b798/trailblazer/cli/core.py#L154-L188 |
pytroll/posttroll | posttroll/ns.py | get_pub_addresses | def get_pub_addresses(names=None, timeout=10, nameserver="localhost"):
"""Get the address of the publisher for a given list of publisher *names*
from the nameserver on *nameserver* (localhost by default).
"""
addrs = []
if names is None:
names = ["", ]
for name in names:
then = datetime.now() + timedelta(seconds=timeout)
while datetime.now() < then:
addrs += get_pub_address(name, nameserver=nameserver)
if addrs:
break
time.sleep(.5)
return addrs | python | def get_pub_addresses(names=None, timeout=10, nameserver="localhost"):
"""Get the address of the publisher for a given list of publisher *names*
from the nameserver on *nameserver* (localhost by default).
"""
addrs = []
if names is None:
names = ["", ]
for name in names:
then = datetime.now() + timedelta(seconds=timeout)
while datetime.now() < then:
addrs += get_pub_address(name, nameserver=nameserver)
if addrs:
break
time.sleep(.5)
return addrs | [
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pytroll/posttroll | posttroll/ns.py | get_pub_address | def get_pub_address(name, timeout=10, nameserver="localhost"):
"""Get the address of the publisher for a given publisher *name* from the
nameserver on *nameserver* (localhost by default).
"""
# Socket to talk to server
socket = get_context().socket(REQ)
try:
socket.setsockopt(LINGER, timeout * 1000)
socket.connect("tcp://" + nameserver + ":" + str(PORT))
logger.debug('Connecting to %s',
"tcp://" + nameserver + ":" + str(PORT))
poller = Poller()
poller.register(socket, POLLIN)
message = Message("/oper/ns", "request", {"service": name})
socket.send_string(six.text_type(message))
# Get the reply.
sock = poller.poll(timeout=timeout * 1000)
if sock:
if sock[0][0] == socket:
message = Message.decode(socket.recv_string(NOBLOCK))
return message.data
else:
raise TimeoutError("Didn't get an address after %d seconds."
% timeout)
finally:
socket.close() | python | def get_pub_address(name, timeout=10, nameserver="localhost"):
"""Get the address of the publisher for a given publisher *name* from the
nameserver on *nameserver* (localhost by default).
"""
# Socket to talk to server
socket = get_context().socket(REQ)
try:
socket.setsockopt(LINGER, timeout * 1000)
socket.connect("tcp://" + nameserver + ":" + str(PORT))
logger.debug('Connecting to %s',
"tcp://" + nameserver + ":" + str(PORT))
poller = Poller()
poller.register(socket, POLLIN)
message = Message("/oper/ns", "request", {"service": name})
socket.send_string(six.text_type(message))
# Get the reply.
sock = poller.poll(timeout=timeout * 1000)
if sock:
if sock[0][0] == socket:
message = Message.decode(socket.recv_string(NOBLOCK))
return message.data
else:
raise TimeoutError("Didn't get an address after %d seconds."
% timeout)
finally:
socket.close() | [
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pytroll/posttroll | posttroll/ns.py | get_active_address | def get_active_address(name, arec):
"""Get the addresses of the active modules for a given publisher *name*.
"""
addrs = arec.get(name)
if addrs:
return Message("/oper/ns", "info", addrs)
else:
return Message("/oper/ns", "info", "") | python | def get_active_address(name, arec):
"""Get the addresses of the active modules for a given publisher *name*.
"""
addrs = arec.get(name)
if addrs:
return Message("/oper/ns", "info", addrs)
else:
return Message("/oper/ns", "info", "") | [
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pytroll/posttroll | posttroll/ns.py | NameServer.run | def run(self, *args):
"""Run the listener and answer to requests.
"""
del args
arec = AddressReceiver(max_age=self._max_age,
multicast_enabled=self._multicast_enabled)
arec.start()
port = PORT
try:
with nslock:
self.listener = get_context().socket(REP)
self.listener.bind("tcp://*:" + str(port))
logger.debug('Listening on port %s', str(port))
poller = Poller()
poller.register(self.listener, POLLIN)
while self.loop:
with nslock:
socks = dict(poller.poll(1000))
if socks:
if socks.get(self.listener) == POLLIN:
msg = self.listener.recv_string()
else:
continue
logger.debug("Replying to request: " + str(msg))
msg = Message.decode(msg)
self.listener.send_unicode(six.text_type(get_active_address(
msg.data["service"], arec)))
except KeyboardInterrupt:
# Needed to stop the nameserver.
pass
finally:
arec.stop()
self.stop() | python | def run(self, *args):
"""Run the listener and answer to requests.
"""
del args
arec = AddressReceiver(max_age=self._max_age,
multicast_enabled=self._multicast_enabled)
arec.start()
port = PORT
try:
with nslock:
self.listener = get_context().socket(REP)
self.listener.bind("tcp://*:" + str(port))
logger.debug('Listening on port %s', str(port))
poller = Poller()
poller.register(self.listener, POLLIN)
while self.loop:
with nslock:
socks = dict(poller.poll(1000))
if socks:
if socks.get(self.listener) == POLLIN:
msg = self.listener.recv_string()
else:
continue
logger.debug("Replying to request: " + str(msg))
msg = Message.decode(msg)
self.listener.send_unicode(six.text_type(get_active_address(
msg.data["service"], arec)))
except KeyboardInterrupt:
# Needed to stop the nameserver.
pass
finally:
arec.stop()
self.stop() | [
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pytroll/posttroll | posttroll/ns.py | NameServer.stop | def stop(self):
"""Stop the name server.
"""
self.listener.setsockopt(LINGER, 1)
self.loop = False
with nslock:
self.listener.close() | python | def stop(self):
"""Stop the name server.
"""
self.listener.setsockopt(LINGER, 1)
self.loop = False
with nslock:
self.listener.close() | [
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zeroSteiner/smoke-zephyr | smoke_zephyr/requirements.py | check_requirements | def check_requirements(requirements, ignore=None):
"""
Parse requirements for package information to determine if all requirements
are met. The *requirements* argument can be a string to a requirements file,
a file like object to be read, or a list of strings representing the package
requirements.
:param requirements: The file to parse.
:type requirements: file obj, list, str, tuple
:param ignore: A sequence of packages to ignore.
:type ignore: list, tuple
:return: A list of missing or incompatible packages.
:rtype: list
"""
ignore = (ignore or [])
not_satisfied = []
working_set = pkg_resources.working_set
installed_packages = dict((p.project_name, p) for p in working_set) # pylint: disable=E1133
if isinstance(requirements, str):
with open(requirements, 'r') as file_h:
requirements = file_h.readlines()
elif hasattr(requirements, 'readlines'):
requirements = requirements.readlines()
elif not isinstance(requirements, (list, tuple)):
raise TypeError('invalid type for argument requirements')
for req_line in requirements:
req_line = req_line.strip()
parts = re.match(r'^([\w\-]+)(([<>=]=)(\d+(\.\d+)*))?$', req_line)
if not parts:
raise ValueError("requirement '{0}' is in an invalid format".format(req_line))
req_pkg = parts.group(1)
if req_pkg in ignore:
continue
if req_pkg not in installed_packages:
try:
find_result = working_set.find(pkg_resources.Requirement.parse(req_line))
except pkg_resources.ResolutionError:
find_result = False
if not find_result:
not_satisfied.append(req_pkg)
continue
if not parts.group(2):
continue
req_version = distutils.version.StrictVersion(parts.group(4))
installed_pkg = installed_packages[req_pkg]
installed_version = re.match(r'^((\d+\.)*\d+)', installed_pkg.version)
if not installed_version:
not_satisfied.append(req_pkg)
continue
installed_version = distutils.version.StrictVersion(installed_version.group(0))
if parts.group(3) == '==' and installed_version != req_version:
not_satisfied.append(req_pkg)
elif parts.group(3) == '>=' and installed_version < req_version:
not_satisfied.append(req_pkg)
elif parts.group(3) == '<=' and installed_version > req_version:
not_satisfied.append(req_pkg)
return not_satisfied | python | def check_requirements(requirements, ignore=None):
"""
Parse requirements for package information to determine if all requirements
are met. The *requirements* argument can be a string to a requirements file,
a file like object to be read, or a list of strings representing the package
requirements.
:param requirements: The file to parse.
:type requirements: file obj, list, str, tuple
:param ignore: A sequence of packages to ignore.
:type ignore: list, tuple
:return: A list of missing or incompatible packages.
:rtype: list
"""
ignore = (ignore or [])
not_satisfied = []
working_set = pkg_resources.working_set
installed_packages = dict((p.project_name, p) for p in working_set) # pylint: disable=E1133
if isinstance(requirements, str):
with open(requirements, 'r') as file_h:
requirements = file_h.readlines()
elif hasattr(requirements, 'readlines'):
requirements = requirements.readlines()
elif not isinstance(requirements, (list, tuple)):
raise TypeError('invalid type for argument requirements')
for req_line in requirements:
req_line = req_line.strip()
parts = re.match(r'^([\w\-]+)(([<>=]=)(\d+(\.\d+)*))?$', req_line)
if not parts:
raise ValueError("requirement '{0}' is in an invalid format".format(req_line))
req_pkg = parts.group(1)
if req_pkg in ignore:
continue
if req_pkg not in installed_packages:
try:
find_result = working_set.find(pkg_resources.Requirement.parse(req_line))
except pkg_resources.ResolutionError:
find_result = False
if not find_result:
not_satisfied.append(req_pkg)
continue
if not parts.group(2):
continue
req_version = distutils.version.StrictVersion(parts.group(4))
installed_pkg = installed_packages[req_pkg]
installed_version = re.match(r'^((\d+\.)*\d+)', installed_pkg.version)
if not installed_version:
not_satisfied.append(req_pkg)
continue
installed_version = distutils.version.StrictVersion(installed_version.group(0))
if parts.group(3) == '==' and installed_version != req_version:
not_satisfied.append(req_pkg)
elif parts.group(3) == '>=' and installed_version < req_version:
not_satisfied.append(req_pkg)
elif parts.group(3) == '<=' and installed_version > req_version:
not_satisfied.append(req_pkg)
return not_satisfied | [
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a file like object to be read, or a list of strings representing the package
requirements.
:param requirements: The file to parse.
:type requirements: file obj, list, str, tuple
:param ignore: A sequence of packages to ignore.
:type ignore: list, tuple
:return: A list of missing or incompatible packages.
:rtype: list | [
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andrewda/frc-livescore | livescore/simpleocr_utils/segmentation.py | segments_from_numpy | def segments_from_numpy(segments):
"""reverses segments_to_numpy"""
segments = segments if SEGMENTS_DIRECTION == 0 else segments.tranpose()
segments = [map(int, s) for s in segments]
return segments | python | def segments_from_numpy(segments):
"""reverses segments_to_numpy"""
segments = segments if SEGMENTS_DIRECTION == 0 else segments.tranpose()
segments = [map(int, s) for s in segments]
return segments | [
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andrewda/frc-livescore | livescore/simpleocr_utils/segmentation.py | segments_to_numpy | def segments_to_numpy(segments):
"""given a list of 4-element tuples, transforms it into a numpy array"""
segments = numpy.array(segments, dtype=SEGMENT_DATATYPE, ndmin=2) # each segment in a row
segments = segments if SEGMENTS_DIRECTION == 0 else numpy.transpose(segments)
return segments | python | def segments_to_numpy(segments):
"""given a list of 4-element tuples, transforms it into a numpy array"""
segments = numpy.array(segments, dtype=SEGMENT_DATATYPE, ndmin=2) # each segment in a row
segments = segments if SEGMENTS_DIRECTION == 0 else numpy.transpose(segments)
return segments | [
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"""given a segment (rectangle) and an image, returns it's corresponding subimage"""
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return image[y:y + h, x:x + w] | python | def region_from_segment(image, segment):
"""given a segment (rectangle) and an image, returns it's corresponding subimage"""
x, y, w, h = segment
return image[y:y + h, x:x + w] | [
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thespacedoctor/sherlock | sherlock/imports/marshall.py | marshall.ingest | def ingest(self):
"""*Ingest the ePESSTO Marshall transient stream into the catalogues database*
The method first creates the tables for the various marshall feeder surveys in the sherlock-catalogues database (if they do not yet exist). Then the marshall database is queried for each transient survey and the results imported into the sherlock-catalogues tables,
See the class docstring for usage
.. todo ::
- convert the directory_script_runner to 'load in file'
"""
self.log.debug('starting the ``get`` method')
# A YAML DICTIONARY OF sherlock-catalogues TABLE NAME AND THE SELECT
# QUERY TO LIFT THE DATA FROM THE MARSHALL
yamlFilePath = '/'.join(string.split(__file__, '/')
[:-1]) + "/resources/pessto_marshall_table_selects.yaml"
stream = file(yamlFilePath, 'r')
marshallQueries = yaml.load(stream)
stream.close()
self.primaryIdColumnName = "primaryId"
self.raColName = "raDeg"
self.declColName = "decDeg"
# CREATE THE MARSHALL IMPORT CATALOGUE TABLES (IF THEY DO NOT EXIST)
directory_script_runner(
log=self.log,
pathToScriptDirectory='/'.join(string.split(__file__,
'/')[:-1]) + "/resources",
databaseName=self.settings["database settings"][
"static catalogues"]["db"],
loginPath=self.settings["database settings"][
"static catalogues"]["loginPath"],
successRule="delete",
failureRule="failed"
)
for k, v in marshallQueries["pessto queries"].iteritems():
self.dbTableName = k
self.databaseInsertbatchSize = 500
dictList = self._create_dictionary_of_marshall(
marshallQuery=v["query"],
marshallTable=v["marshallTable"]
)
tableName = self.dbTableName
self.add_data_to_database_table(
dictList=dictList
)
self.log.debug('completed the ``get`` method')
return None | python | def ingest(self):
"""*Ingest the ePESSTO Marshall transient stream into the catalogues database*
The method first creates the tables for the various marshall feeder surveys in the sherlock-catalogues database (if they do not yet exist). Then the marshall database is queried for each transient survey and the results imported into the sherlock-catalogues tables,
See the class docstring for usage
.. todo ::
- convert the directory_script_runner to 'load in file'
"""
self.log.debug('starting the ``get`` method')
# A YAML DICTIONARY OF sherlock-catalogues TABLE NAME AND THE SELECT
# QUERY TO LIFT THE DATA FROM THE MARSHALL
yamlFilePath = '/'.join(string.split(__file__, '/')
[:-1]) + "/resources/pessto_marshall_table_selects.yaml"
stream = file(yamlFilePath, 'r')
marshallQueries = yaml.load(stream)
stream.close()
self.primaryIdColumnName = "primaryId"
self.raColName = "raDeg"
self.declColName = "decDeg"
# CREATE THE MARSHALL IMPORT CATALOGUE TABLES (IF THEY DO NOT EXIST)
directory_script_runner(
log=self.log,
pathToScriptDirectory='/'.join(string.split(__file__,
'/')[:-1]) + "/resources",
databaseName=self.settings["database settings"][
"static catalogues"]["db"],
loginPath=self.settings["database settings"][
"static catalogues"]["loginPath"],
successRule="delete",
failureRule="failed"
)
for k, v in marshallQueries["pessto queries"].iteritems():
self.dbTableName = k
self.databaseInsertbatchSize = 500
dictList = self._create_dictionary_of_marshall(
marshallQuery=v["query"],
marshallTable=v["marshallTable"]
)
tableName = self.dbTableName
self.add_data_to_database_table(
dictList=dictList
)
self.log.debug('completed the ``get`` method')
return None | [
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See the class docstring for usage
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thespacedoctor/sherlock | sherlock/imports/marshall.py | marshall._create_dictionary_of_marshall | def _create_dictionary_of_marshall(
self,
marshallQuery,
marshallTable):
"""create a list of dictionaries containing all the rows in the marshall stream
**Key Arguments:**
- ``marshallQuery`` -- the query used to lift the required data from the marshall database.
- ``marshallTable`` -- the name of the marshall table we are lifting the data from.
**Return:**
- ``dictList`` - a list of dictionaries containing all the rows in the marshall stream
"""
self.log.debug(
'starting the ``_create_dictionary_of_marshall`` method')
dictList = []
tableName = self.dbTableName
rows = readquery(
log=self.log,
sqlQuery=marshallQuery,
dbConn=self.pmDbConn,
quiet=False
)
totalCount = len(rows)
count = 0
for row in rows:
if "dateCreated" in row:
del row["dateCreated"]
count += 1
if count > 1:
# Cursor up one line and clear line
sys.stdout.write("\x1b[1A\x1b[2K")
print "%(count)s / %(totalCount)s `%(tableName)s` data added to memory" % locals()
dictList.append(dict(row))
self.log.debug(
'completed the ``_create_dictionary_of_marshall`` method')
return dictList | python | def _create_dictionary_of_marshall(
self,
marshallQuery,
marshallTable):
"""create a list of dictionaries containing all the rows in the marshall stream
**Key Arguments:**
- ``marshallQuery`` -- the query used to lift the required data from the marshall database.
- ``marshallTable`` -- the name of the marshall table we are lifting the data from.
**Return:**
- ``dictList`` - a list of dictionaries containing all the rows in the marshall stream
"""
self.log.debug(
'starting the ``_create_dictionary_of_marshall`` method')
dictList = []
tableName = self.dbTableName
rows = readquery(
log=self.log,
sqlQuery=marshallQuery,
dbConn=self.pmDbConn,
quiet=False
)
totalCount = len(rows)
count = 0
for row in rows:
if "dateCreated" in row:
del row["dateCreated"]
count += 1
if count > 1:
# Cursor up one line and clear line
sys.stdout.write("\x1b[1A\x1b[2K")
print "%(count)s / %(totalCount)s `%(tableName)s` data added to memory" % locals()
dictList.append(dict(row))
self.log.debug(
'completed the ``_create_dictionary_of_marshall`` method')
return dictList | [
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- ``marshallTable`` -- the name of the marshall table we are lifting the data from.
**Return:**
- ``dictList`` - a list of dictionaries containing all the rows in the marshall stream | [
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thespacedoctor/sherlock | sherlock/imports/ned_d.py | ned_d.ingest | def ingest(self):
"""Import the ned_d catalogue into the catalogues database
The method first generates a list of python dictionaries from the ned_d datafile, imports this list of dictionaries into a database table and then generates the HTMIDs for that table.
**Usage:**
See class docstring for usage
.. todo ::
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``get`` method')
dictList = self._create_dictionary_of_ned_d()
self.primaryIdColumnName = "primaryId"
self.raColName = "raDeg"
self.declColName = "decDeg"
tableName = self.dbTableName
createStatement = u"""
CREATE TABLE `%(tableName)s` (
`primaryId` bigint(20) NOT NULL AUTO_INCREMENT COMMENT 'An internal counter',
`Method` varchar(150) DEFAULT NULL,
`dateCreated` datetime DEFAULT CURRENT_TIMESTAMP,
`dateLastModified` datetime DEFAULT CURRENT_TIMESTAMP,
`updated` varchar(45) DEFAULT '0',
`dist_derived_from_sn` varchar(150) DEFAULT NULL,
`dist_in_ned_flag` varchar(10) DEFAULT NULL,
`dist_index_id` mediumint(9) DEFAULT NULL,
`dist_mod` double DEFAULT NULL,
`dist_mod_err` double DEFAULT NULL,
`dist_mpc` double DEFAULT NULL,
`galaxy_index_id` mediumint(9) DEFAULT NULL,
`hubble_const` double DEFAULT NULL,
`lmc_mod` double DEFAULT NULL,
`notes` varchar(500) DEFAULT NULL,
`primary_ned_id` varchar(150) DEFAULT NULL,
`redshift` double DEFAULT NULL,
`ref` varchar(150) DEFAULT NULL,
`ref_date` int(11) DEFAULT NULL,
`master_row` tinyint(4) DEFAULT '0',
`major_diameter_arcmin` double DEFAULT NULL,
`ned_notes` varchar(700) DEFAULT NULL,
`object_type` varchar(100) DEFAULT NULL,
`redshift_err` double DEFAULT NULL,
`redshift_quality` varchar(100) DEFAULT NULL,
`magnitude_filter` varchar(10) DEFAULT NULL,
`minor_diameter_arcmin` double DEFAULT NULL,
`morphology` varchar(50) DEFAULT NULL,
`hierarchy` varchar(50) DEFAULT NULL,
`galaxy_morphology` varchar(50) DEFAULT NULL,
`radio_morphology` varchar(50) DEFAULT NULL,
`activity_type` varchar(50) DEFAULT NULL,
`in_ned` tinyint(4) DEFAULT NULL,
`raDeg` double DEFAULT NULL,
`decDeg` double DEFAULT NULL,
`eb_v` double DEFAULT NULL,
`sdss_coverage` TINYINT DEFAULT NULL,
PRIMARY KEY (`primaryId`),
UNIQUE KEY `galaxy_index_id_dist_index_id` (`galaxy_index_id`,`dist_index_id`)
) ENGINE=MyISAM AUTO_INCREMENT=0 DEFAULT CHARSET=latin1;
DROP VIEW IF EXISTS `view_%(tableName)s_master_recorders`;
CREATE
VIEW `view_%(tableName)s_master_recorders` AS
(SELECT
`%(tableName)s`.`primary_ned_id` AS `primary_ned_id`,
`%(tableName)s`.`object_type` AS `object_type`,
`%(tableName)s`.`raDeg` AS `raDeg`,
`%(tableName)s`.`decDeg` AS `decDeg`,
`%(tableName)s`.`dist_mpc` AS `dist_mpc`,
`%(tableName)s`.`dist_mod` AS `dist_mod`,
`%(tableName)s`.`dist_mod_err` AS `dist_mod_err`,
`%(tableName)s`.`Method` AS `dist_measurement_method`,
`%(tableName)s`.`redshift` AS `redshift`,
`%(tableName)s`.`redshift_err` AS `redshift_err`,
`%(tableName)s`.`redshift_quality` AS `redshift_quality`,
`%(tableName)s`.`major_diameter_arcmin` AS `major_diameter_arcmin`,
`%(tableName)s`.`minor_diameter_arcmin` AS `minor_diameter_arcmin`,
`%(tableName)s`.`magnitude_filter` AS `magnitude_filter`,
`%(tableName)s`.`eb_v` AS `gal_eb_v`,
`%(tableName)s`.`hierarchy` AS `hierarchy`,
`%(tableName)s`.`morphology` AS `morphology`,
`%(tableName)s`.`radio_morphology` AS `radio_morphology`,
`%(tableName)s`.`activity_type` AS `activity_type`,
`%(tableName)s`.`ned_notes` AS `ned_notes`,
`%(tableName)s`.`in_ned` AS `in_ned`,
`%(tableName)s`.`primaryId` AS `primaryId`
FROM
`%(tableName)s`
WHERE
(`%(tableName)s`.`master_row` = 1));
""" % locals()
self.add_data_to_database_table(
dictList=dictList,
createStatement=createStatement
)
self._clean_up_columns()
self._get_metadata_for_galaxies()
self._update_sdss_coverage()
self.log.debug('completed the ``get`` method')
return None | python | def ingest(self):
"""Import the ned_d catalogue into the catalogues database
The method first generates a list of python dictionaries from the ned_d datafile, imports this list of dictionaries into a database table and then generates the HTMIDs for that table.
**Usage:**
See class docstring for usage
.. todo ::
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``get`` method')
dictList = self._create_dictionary_of_ned_d()
self.primaryIdColumnName = "primaryId"
self.raColName = "raDeg"
self.declColName = "decDeg"
tableName = self.dbTableName
createStatement = u"""
CREATE TABLE `%(tableName)s` (
`primaryId` bigint(20) NOT NULL AUTO_INCREMENT COMMENT 'An internal counter',
`Method` varchar(150) DEFAULT NULL,
`dateCreated` datetime DEFAULT CURRENT_TIMESTAMP,
`dateLastModified` datetime DEFAULT CURRENT_TIMESTAMP,
`updated` varchar(45) DEFAULT '0',
`dist_derived_from_sn` varchar(150) DEFAULT NULL,
`dist_in_ned_flag` varchar(10) DEFAULT NULL,
`dist_index_id` mediumint(9) DEFAULT NULL,
`dist_mod` double DEFAULT NULL,
`dist_mod_err` double DEFAULT NULL,
`dist_mpc` double DEFAULT NULL,
`galaxy_index_id` mediumint(9) DEFAULT NULL,
`hubble_const` double DEFAULT NULL,
`lmc_mod` double DEFAULT NULL,
`notes` varchar(500) DEFAULT NULL,
`primary_ned_id` varchar(150) DEFAULT NULL,
`redshift` double DEFAULT NULL,
`ref` varchar(150) DEFAULT NULL,
`ref_date` int(11) DEFAULT NULL,
`master_row` tinyint(4) DEFAULT '0',
`major_diameter_arcmin` double DEFAULT NULL,
`ned_notes` varchar(700) DEFAULT NULL,
`object_type` varchar(100) DEFAULT NULL,
`redshift_err` double DEFAULT NULL,
`redshift_quality` varchar(100) DEFAULT NULL,
`magnitude_filter` varchar(10) DEFAULT NULL,
`minor_diameter_arcmin` double DEFAULT NULL,
`morphology` varchar(50) DEFAULT NULL,
`hierarchy` varchar(50) DEFAULT NULL,
`galaxy_morphology` varchar(50) DEFAULT NULL,
`radio_morphology` varchar(50) DEFAULT NULL,
`activity_type` varchar(50) DEFAULT NULL,
`in_ned` tinyint(4) DEFAULT NULL,
`raDeg` double DEFAULT NULL,
`decDeg` double DEFAULT NULL,
`eb_v` double DEFAULT NULL,
`sdss_coverage` TINYINT DEFAULT NULL,
PRIMARY KEY (`primaryId`),
UNIQUE KEY `galaxy_index_id_dist_index_id` (`galaxy_index_id`,`dist_index_id`)
) ENGINE=MyISAM AUTO_INCREMENT=0 DEFAULT CHARSET=latin1;
DROP VIEW IF EXISTS `view_%(tableName)s_master_recorders`;
CREATE
VIEW `view_%(tableName)s_master_recorders` AS
(SELECT
`%(tableName)s`.`primary_ned_id` AS `primary_ned_id`,
`%(tableName)s`.`object_type` AS `object_type`,
`%(tableName)s`.`raDeg` AS `raDeg`,
`%(tableName)s`.`decDeg` AS `decDeg`,
`%(tableName)s`.`dist_mpc` AS `dist_mpc`,
`%(tableName)s`.`dist_mod` AS `dist_mod`,
`%(tableName)s`.`dist_mod_err` AS `dist_mod_err`,
`%(tableName)s`.`Method` AS `dist_measurement_method`,
`%(tableName)s`.`redshift` AS `redshift`,
`%(tableName)s`.`redshift_err` AS `redshift_err`,
`%(tableName)s`.`redshift_quality` AS `redshift_quality`,
`%(tableName)s`.`major_diameter_arcmin` AS `major_diameter_arcmin`,
`%(tableName)s`.`minor_diameter_arcmin` AS `minor_diameter_arcmin`,
`%(tableName)s`.`magnitude_filter` AS `magnitude_filter`,
`%(tableName)s`.`eb_v` AS `gal_eb_v`,
`%(tableName)s`.`hierarchy` AS `hierarchy`,
`%(tableName)s`.`morphology` AS `morphology`,
`%(tableName)s`.`radio_morphology` AS `radio_morphology`,
`%(tableName)s`.`activity_type` AS `activity_type`,
`%(tableName)s`.`ned_notes` AS `ned_notes`,
`%(tableName)s`.`in_ned` AS `in_ned`,
`%(tableName)s`.`primaryId` AS `primaryId`
FROM
`%(tableName)s`
WHERE
(`%(tableName)s`.`master_row` = 1));
""" % locals()
self.add_data_to_database_table(
dictList=dictList,
createStatement=createStatement
)
self._clean_up_columns()
self._get_metadata_for_galaxies()
self._update_sdss_coverage()
self.log.debug('completed the ``get`` method')
return None | [
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] | Import the ned_d catalogue into the catalogues database
The method first generates a list of python dictionaries from the ned_d datafile, imports this list of dictionaries into a database table and then generates the HTMIDs for that table.
**Usage:**
See class docstring for usage
.. todo ::
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring | [
"Import",
"the",
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"database"
] | train | https://github.com/thespacedoctor/sherlock/blob/2c80fb6fa31b04e7820e6928e3d437a21e692dd3/sherlock/imports/ned_d.py#L66-L175 |
thespacedoctor/sherlock | sherlock/imports/ned_d.py | ned_d._create_dictionary_of_ned_d | def _create_dictionary_of_ned_d(
self):
"""create a list of dictionaries containing all the rows in the ned_d catalogue
**Return:**
- ``dictList`` - a list of dictionaries containing all the rows in the ned_d catalogue
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug(
'starting the ``_create_dictionary_of_ned_d`` method')
count = 0
with open(self.pathToDataFile, 'rb') as csvFile:
csvReader = csv.reader(
csvFile, dialect='excel', delimiter=',', quotechar='"')
totalRows = sum(1 for row in csvReader)
csvFile.close()
totalCount = totalRows
with open(self.pathToDataFile, 'rb') as csvFile:
csvReader = csv.reader(
csvFile, dialect='excel', delimiter=',', quotechar='"')
theseKeys = []
dictList = []
for row in csvReader:
if len(theseKeys) == 0:
totalRows -= 1
if "Exclusion Code" in row and "Hubble const." in row:
for i in row:
if i == "redshift (z)":
theseKeys.append("redshift")
elif i == "Hubble const.":
theseKeys.append("hubble_const")
elif i == "G":
theseKeys.append("galaxy_index_id")
elif i == "err":
theseKeys.append("dist_mod_err")
elif i == "D (Mpc)":
theseKeys.append("dist_mpc")
elif i == "Date (Yr. - 1980)":
theseKeys.append("ref_date")
elif i == "REFCODE":
theseKeys.append("ref")
elif i == "Exclusion Code":
theseKeys.append("dist_in_ned_flag")
elif i == "Adopted LMC modulus":
theseKeys.append("lmc_mod")
elif i == "m-M":
theseKeys.append("dist_mod")
elif i == "Notes":
theseKeys.append("notes")
elif i == "SN ID":
theseKeys.append("dist_derived_from_sn")
elif i == "method":
theseKeys.append("dist_method")
elif i == "Galaxy ID":
theseKeys.append("primary_ned_id")
elif i == "D":
theseKeys.append("dist_index_id")
else:
theseKeys.append(i)
continue
if len(theseKeys):
count += 1
if count > 1:
# Cursor up one line and clear line
sys.stdout.write("\x1b[1A\x1b[2K")
if count > totalCount:
count = totalCount
percent = (float(count) / float(totalCount)) * 100.
print "%(count)s / %(totalCount)s (%(percent)1.1f%%) rows added to memory" % locals()
rowDict = {}
for t, r in zip(theseKeys, row):
rowDict[t] = r
if t == "ref_date":
try:
rowDict[t] = int(r) + 1980
except:
rowDict[t] = None
if rowDict["dist_index_id"] != "999999":
dictList.append(rowDict)
csvFile.close()
self.log.debug(
'completed the ``_create_dictionary_of_ned_d`` method')
return dictList | python | def _create_dictionary_of_ned_d(
self):
"""create a list of dictionaries containing all the rows in the ned_d catalogue
**Return:**
- ``dictList`` - a list of dictionaries containing all the rows in the ned_d catalogue
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug(
'starting the ``_create_dictionary_of_ned_d`` method')
count = 0
with open(self.pathToDataFile, 'rb') as csvFile:
csvReader = csv.reader(
csvFile, dialect='excel', delimiter=',', quotechar='"')
totalRows = sum(1 for row in csvReader)
csvFile.close()
totalCount = totalRows
with open(self.pathToDataFile, 'rb') as csvFile:
csvReader = csv.reader(
csvFile, dialect='excel', delimiter=',', quotechar='"')
theseKeys = []
dictList = []
for row in csvReader:
if len(theseKeys) == 0:
totalRows -= 1
if "Exclusion Code" in row and "Hubble const." in row:
for i in row:
if i == "redshift (z)":
theseKeys.append("redshift")
elif i == "Hubble const.":
theseKeys.append("hubble_const")
elif i == "G":
theseKeys.append("galaxy_index_id")
elif i == "err":
theseKeys.append("dist_mod_err")
elif i == "D (Mpc)":
theseKeys.append("dist_mpc")
elif i == "Date (Yr. - 1980)":
theseKeys.append("ref_date")
elif i == "REFCODE":
theseKeys.append("ref")
elif i == "Exclusion Code":
theseKeys.append("dist_in_ned_flag")
elif i == "Adopted LMC modulus":
theseKeys.append("lmc_mod")
elif i == "m-M":
theseKeys.append("dist_mod")
elif i == "Notes":
theseKeys.append("notes")
elif i == "SN ID":
theseKeys.append("dist_derived_from_sn")
elif i == "method":
theseKeys.append("dist_method")
elif i == "Galaxy ID":
theseKeys.append("primary_ned_id")
elif i == "D":
theseKeys.append("dist_index_id")
else:
theseKeys.append(i)
continue
if len(theseKeys):
count += 1
if count > 1:
# Cursor up one line and clear line
sys.stdout.write("\x1b[1A\x1b[2K")
if count > totalCount:
count = totalCount
percent = (float(count) / float(totalCount)) * 100.
print "%(count)s / %(totalCount)s (%(percent)1.1f%%) rows added to memory" % locals()
rowDict = {}
for t, r in zip(theseKeys, row):
rowDict[t] = r
if t == "ref_date":
try:
rowDict[t] = int(r) + 1980
except:
rowDict[t] = None
if rowDict["dist_index_id"] != "999999":
dictList.append(rowDict)
csvFile.close()
self.log.debug(
'completed the ``_create_dictionary_of_ned_d`` method')
return dictList | [
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] | create a list of dictionaries containing all the rows in the ned_d catalogue
**Return:**
- ``dictList`` - a list of dictionaries containing all the rows in the ned_d catalogue
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring | [
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] | train | https://github.com/thespacedoctor/sherlock/blob/2c80fb6fa31b04e7820e6928e3d437a21e692dd3/sherlock/imports/ned_d.py#L177-L274 |
thespacedoctor/sherlock | sherlock/imports/ned_d.py | ned_d._clean_up_columns | def _clean_up_columns(
self):
"""clean up columns of the NED table
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_clean_up_columns`` method')
tableName = self.dbTableName
print "cleaning up %(tableName)s columns" % locals()
sqlQuery = u"""
set sql_mode="STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION";
""" % locals()
writequery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
)
sqlQuery = u"""
update %(tableName)s set dist_mod_err = null where dist_mod_err = 0;
update %(tableName)s set dist_in_ned_flag = null where dist_in_ned_flag = "";
update %(tableName)s set notes = null where notes = "";
update %(tableName)s set redshift = null where redshift = 0;
update %(tableName)s set dist_derived_from_sn = null where dist_derived_from_sn = "";
update %(tableName)s set hubble_const = null where hubble_const = 0;
update %(tableName)s set lmc_mod = null where lmc_mod = 0;
update %(tableName)s set master_row = 0;
update %(tableName)s set master_row = 1 where primaryId in (select * from (select distinct primaryId from %(tableName)s group by galaxy_index_id) as alias);
""" % locals()
writequery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
)
self.log.debug('completed the ``_clean_up_columns`` method')
return None | python | def _clean_up_columns(
self):
"""clean up columns of the NED table
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_clean_up_columns`` method')
tableName = self.dbTableName
print "cleaning up %(tableName)s columns" % locals()
sqlQuery = u"""
set sql_mode="STRICT_TRANS_TABLES,NO_ZERO_IN_DATE,NO_ZERO_DATE,ERROR_FOR_DIVISION_BY_ZERO,NO_AUTO_CREATE_USER,NO_ENGINE_SUBSTITUTION";
""" % locals()
writequery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
)
sqlQuery = u"""
update %(tableName)s set dist_mod_err = null where dist_mod_err = 0;
update %(tableName)s set dist_in_ned_flag = null where dist_in_ned_flag = "";
update %(tableName)s set notes = null where notes = "";
update %(tableName)s set redshift = null where redshift = 0;
update %(tableName)s set dist_derived_from_sn = null where dist_derived_from_sn = "";
update %(tableName)s set hubble_const = null where hubble_const = 0;
update %(tableName)s set lmc_mod = null where lmc_mod = 0;
update %(tableName)s set master_row = 0;
update %(tableName)s set master_row = 1 where primaryId in (select * from (select distinct primaryId from %(tableName)s group by galaxy_index_id) as alias);
""" % locals()
writequery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
)
self.log.debug('completed the ``_clean_up_columns`` method')
return None | [
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.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring | [
"clean",
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"columns",
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] | train | https://github.com/thespacedoctor/sherlock/blob/2c80fb6fa31b04e7820e6928e3d437a21e692dd3/sherlock/imports/ned_d.py#L276-L323 |
thespacedoctor/sherlock | sherlock/imports/ned_d.py | ned_d._get_metadata_for_galaxies | def _get_metadata_for_galaxies(
self):
"""get metadata for galaxies
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_get_metadata_for_galaxies`` method')
total, batches = self._count_galaxies_requiring_metadata()
print "%(total)s galaxies require metadata. Need to send %(batches)s batch requests to NED." % locals()
totalBatches = self.batches
thisCount = 0
# FOR EACH BATCH, GET THE GALAXY IDs, QUERY NED AND UPDATE THE DATABASE
while self.total:
thisCount += 1
self._get_3000_galaxies_needing_metadata()
dictList = self._query_ned_and_add_results_to_database(thisCount)
self.add_data_to_database_table(
dictList=dictList,
createStatement=False
)
self._count_galaxies_requiring_metadata()
self.log.debug('completed the ``_get_metadata_for_galaxies`` method')
return None | python | def _get_metadata_for_galaxies(
self):
"""get metadata for galaxies
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_get_metadata_for_galaxies`` method')
total, batches = self._count_galaxies_requiring_metadata()
print "%(total)s galaxies require metadata. Need to send %(batches)s batch requests to NED." % locals()
totalBatches = self.batches
thisCount = 0
# FOR EACH BATCH, GET THE GALAXY IDs, QUERY NED AND UPDATE THE DATABASE
while self.total:
thisCount += 1
self._get_3000_galaxies_needing_metadata()
dictList = self._query_ned_and_add_results_to_database(thisCount)
self.add_data_to_database_table(
dictList=dictList,
createStatement=False
)
self._count_galaxies_requiring_metadata()
self.log.debug('completed the ``_get_metadata_for_galaxies`` method')
return None | [
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.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring | [
"get",
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] | train | https://github.com/thespacedoctor/sherlock/blob/2c80fb6fa31b04e7820e6928e3d437a21e692dd3/sherlock/imports/ned_d.py#L325-L361 |
thespacedoctor/sherlock | sherlock/imports/ned_d.py | ned_d._get_3000_galaxies_needing_metadata | def _get_3000_galaxies_needing_metadata(
self):
""" get 3000 galaxies needing metadata
**Return:**
- ``len(self.theseIds)`` -- the number of NED IDs returned
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug(
'starting the ``_get_3000_galaxies_needing_metadata`` method')
tableName = self.dbTableName
# SELECT THE DATA FROM NED TABLE
self.theseIds = {}
sqlQuery = u"""
select primaryId, primary_ned_id from %(tableName)s where master_row = 1 and in_ned is null limit 3000;
""" % locals()
rows = readquery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
quiet=False
)
for row in rows:
self.theseIds[row["primary_ned_id"]] = row["primaryId"]
self.log.debug(
'completed the ``_get_3000_galaxies_needing_metadata`` method')
return len(self.theseIds) | python | def _get_3000_galaxies_needing_metadata(
self):
""" get 3000 galaxies needing metadata
**Return:**
- ``len(self.theseIds)`` -- the number of NED IDs returned
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug(
'starting the ``_get_3000_galaxies_needing_metadata`` method')
tableName = self.dbTableName
# SELECT THE DATA FROM NED TABLE
self.theseIds = {}
sqlQuery = u"""
select primaryId, primary_ned_id from %(tableName)s where master_row = 1 and in_ned is null limit 3000;
""" % locals()
rows = readquery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
quiet=False
)
for row in rows:
self.theseIds[row["primary_ned_id"]] = row["primaryId"]
self.log.debug(
'completed the ``_get_3000_galaxies_needing_metadata`` method')
return len(self.theseIds) | [
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**Return:**
- ``len(self.theseIds)`` -- the number of NED IDs returned
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring | [
"get",
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] | train | https://github.com/thespacedoctor/sherlock/blob/2c80fb6fa31b04e7820e6928e3d437a21e692dd3/sherlock/imports/ned_d.py#L404-L443 |
thespacedoctor/sherlock | sherlock/imports/ned_d.py | ned_d._query_ned_and_add_results_to_database | def _query_ned_and_add_results_to_database(
self,
batchCount):
""" query ned and add results to database
**Key Arguments:**
- ``batchCount`` - the index number of the batch sent to NED
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug(
'starting the ``_query_ned_and_add_results_to_database`` method')
tableName = self.dbTableName
# ASTROCALC UNIT CONVERTER OBJECT
converter = unit_conversion(
log=self.log
)
# QUERY NED WITH BATCH
totalCount = len(self.theseIds)
print "requesting metadata from NED for %(totalCount)s galaxies (batch %(batchCount)s)" % locals()
search = namesearch(
log=self.log,
names=self.theseIds.keys(),
quiet=True
)
results = search.get()
print "results returned from ned -- starting to add to database" % locals()
# CLEAN THE RETURNED DATA AND UPDATE DATABASE
totalCount = len(results)
count = 0
sqlQuery = ""
dictList = []
colList = ["redshift_quality", "redshift", "hierarchy", "object_type", "major_diameter_arcmin", "morphology", "magnitude_filter",
"ned_notes", "eb_v", "raDeg", "radio_morphology", "activity_type", "minor_diameter_arcmin", "decDeg", "redshift_err", "in_ned"]
if not len(results):
for k, v in self.theseIds.iteritems():
dictList.append({
"in_ned": 0,
"primaryID": v
})
for thisDict in results:
thisDict["tableName"] = tableName
count += 1
for k, v in thisDict.iteritems():
if not v or len(v) == 0:
thisDict[k] = "null"
if k in ["major_diameter_arcmin", "minor_diameter_arcmin"] and (":" in v or "?" in v or "<" in v):
thisDict[k] = v.replace(":", "").replace(
"?", "").replace("<", "")
if isinstance(v, str) and '"' in v:
thisDict[k] = v.replace('"', '\\"')
if "Input name not" not in thisDict["input_note"] and "Same object as" not in thisDict["input_note"]:
if thisDict["ra"] != "null" and thisDict["dec"] != "null":
thisDict["raDeg"] = converter.ra_sexegesimal_to_decimal(
ra=thisDict["ra"]
)
thisDict["decDeg"] = converter.dec_sexegesimal_to_decimal(
dec=thisDict["dec"]
)
else:
thisDict["raDeg"] = None
thisDict["decDeg"] = None
thisDict["in_ned"] = 1
thisDict["eb_v"] = thisDict["eb-v"]
row = {}
row["primary_ned_id"] = thisDict["input_name"]
try:
row["primaryID"] = self.theseIds[thisDict["input_name"]]
for c in colList:
if thisDict[c] == "null":
row[c] = None
else:
row[c] = thisDict[c]
dictList.append(row)
except:
g = thisDict["input_name"]
self.log.error(
"Cannot find database table %(tableName)s primaryID for '%(g)s'\n\n" % locals())
dictList.append({
"in_ned": 0,
"primary_ned_id": thisDict["input_name"]
})
else:
dictList.append({
"primary_ned_id": thisDict["input_name"],
"in_ned": 0,
"primaryID": self.theseIds[thisDict["input_name"]]
})
self.log.debug(
'completed the ``_query_ned_and_add_results_to_database`` method')
return dictList | python | def _query_ned_and_add_results_to_database(
self,
batchCount):
""" query ned and add results to database
**Key Arguments:**
- ``batchCount`` - the index number of the batch sent to NED
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug(
'starting the ``_query_ned_and_add_results_to_database`` method')
tableName = self.dbTableName
# ASTROCALC UNIT CONVERTER OBJECT
converter = unit_conversion(
log=self.log
)
# QUERY NED WITH BATCH
totalCount = len(self.theseIds)
print "requesting metadata from NED for %(totalCount)s galaxies (batch %(batchCount)s)" % locals()
search = namesearch(
log=self.log,
names=self.theseIds.keys(),
quiet=True
)
results = search.get()
print "results returned from ned -- starting to add to database" % locals()
# CLEAN THE RETURNED DATA AND UPDATE DATABASE
totalCount = len(results)
count = 0
sqlQuery = ""
dictList = []
colList = ["redshift_quality", "redshift", "hierarchy", "object_type", "major_diameter_arcmin", "morphology", "magnitude_filter",
"ned_notes", "eb_v", "raDeg", "radio_morphology", "activity_type", "minor_diameter_arcmin", "decDeg", "redshift_err", "in_ned"]
if not len(results):
for k, v in self.theseIds.iteritems():
dictList.append({
"in_ned": 0,
"primaryID": v
})
for thisDict in results:
thisDict["tableName"] = tableName
count += 1
for k, v in thisDict.iteritems():
if not v or len(v) == 0:
thisDict[k] = "null"
if k in ["major_diameter_arcmin", "minor_diameter_arcmin"] and (":" in v or "?" in v or "<" in v):
thisDict[k] = v.replace(":", "").replace(
"?", "").replace("<", "")
if isinstance(v, str) and '"' in v:
thisDict[k] = v.replace('"', '\\"')
if "Input name not" not in thisDict["input_note"] and "Same object as" not in thisDict["input_note"]:
if thisDict["ra"] != "null" and thisDict["dec"] != "null":
thisDict["raDeg"] = converter.ra_sexegesimal_to_decimal(
ra=thisDict["ra"]
)
thisDict["decDeg"] = converter.dec_sexegesimal_to_decimal(
dec=thisDict["dec"]
)
else:
thisDict["raDeg"] = None
thisDict["decDeg"] = None
thisDict["in_ned"] = 1
thisDict["eb_v"] = thisDict["eb-v"]
row = {}
row["primary_ned_id"] = thisDict["input_name"]
try:
row["primaryID"] = self.theseIds[thisDict["input_name"]]
for c in colList:
if thisDict[c] == "null":
row[c] = None
else:
row[c] = thisDict[c]
dictList.append(row)
except:
g = thisDict["input_name"]
self.log.error(
"Cannot find database table %(tableName)s primaryID for '%(g)s'\n\n" % locals())
dictList.append({
"in_ned": 0,
"primary_ned_id": thisDict["input_name"]
})
else:
dictList.append({
"primary_ned_id": thisDict["input_name"],
"in_ned": 0,
"primaryID": self.theseIds[thisDict["input_name"]]
})
self.log.debug(
'completed the ``_query_ned_and_add_results_to_database`` method')
return dictList | [
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**Key Arguments:**
- ``batchCount`` - the index number of the batch sent to NED
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring | [
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thespacedoctor/sherlock | sherlock/imports/ned_d.py | ned_d._update_sdss_coverage | def _update_sdss_coverage(
self):
""" update sdss coverage
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_update_sdss_coverage`` method')
tableName = self.dbTableName
# SELECT THE LOCATIONS NEEDING TO BE CHECKED
sqlQuery = u"""
select primary_ned_id, primaryID, raDeg, decDeg, sdss_coverage from %(tableName)s where sdss_coverage is null and master_row = 1 and in_ned = 1 order by dist_mpc;
""" % locals()
rows = readquery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
quiet=False
)
totalCount = len(rows)
count = 0
for row in rows:
count += 1
if count > 1:
# Cursor up three lines and clear
sys.stdout.write("\x1b[1A\x1b[2K")
sys.stdout.write("\x1b[1A\x1b[2K")
sys.stdout.write("\x1b[1A\x1b[2K")
if count > totalCount:
count = totalCount
percent = (float(count) / float(totalCount)) * 100.
primaryID = row["primaryID"]
raDeg = float(row["raDeg"])
decDeg = float(row["decDeg"])
primary_ned_id = row["primary_ned_id"]
# SDSS CAN ONLY ACCEPT 60 QUERIES/MIN
time.sleep(1.1)
print "%(count)s / %(totalCount)s (%(percent)1.1f%%) NED galaxies checked for SDSS coverage" % locals()
print "NED NAME: ", primary_ned_id
# covered = True | False | 999 (i.e. not sure)
sdss_coverage = check_coverage(
log=self.log,
ra=raDeg,
dec=decDeg
).get()
if sdss_coverage == 999:
sdss_coverage_flag = "null"
elif sdss_coverage == True:
sdss_coverage_flag = 1
elif sdss_coverage == False:
sdss_coverage_flag = 0
else:
self.log.error('cound not get sdss coverage' % locals())
sys.exit(0)
# UPDATE THE DATABASE FLAG
sqlQuery = u"""
update %(tableName)s set sdss_coverage = %(sdss_coverage_flag)s where primaryID = %(primaryID)s
""" % locals()
writequery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
)
self.log.debug('completed the ``_update_sdss_coverage`` method')
return None | python | def _update_sdss_coverage(
self):
""" update sdss coverage
.. todo ::
- update key arguments values and definitions with defaults
- update return values and definitions
- update usage examples and text
- update docstring text
- check sublime snippet exists
- clip any useful text to docs mindmap
- regenerate the docs and check redendering of this docstring
"""
self.log.debug('starting the ``_update_sdss_coverage`` method')
tableName = self.dbTableName
# SELECT THE LOCATIONS NEEDING TO BE CHECKED
sqlQuery = u"""
select primary_ned_id, primaryID, raDeg, decDeg, sdss_coverage from %(tableName)s where sdss_coverage is null and master_row = 1 and in_ned = 1 order by dist_mpc;
""" % locals()
rows = readquery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
quiet=False
)
totalCount = len(rows)
count = 0
for row in rows:
count += 1
if count > 1:
# Cursor up three lines and clear
sys.stdout.write("\x1b[1A\x1b[2K")
sys.stdout.write("\x1b[1A\x1b[2K")
sys.stdout.write("\x1b[1A\x1b[2K")
if count > totalCount:
count = totalCount
percent = (float(count) / float(totalCount)) * 100.
primaryID = row["primaryID"]
raDeg = float(row["raDeg"])
decDeg = float(row["decDeg"])
primary_ned_id = row["primary_ned_id"]
# SDSS CAN ONLY ACCEPT 60 QUERIES/MIN
time.sleep(1.1)
print "%(count)s / %(totalCount)s (%(percent)1.1f%%) NED galaxies checked for SDSS coverage" % locals()
print "NED NAME: ", primary_ned_id
# covered = True | False | 999 (i.e. not sure)
sdss_coverage = check_coverage(
log=self.log,
ra=raDeg,
dec=decDeg
).get()
if sdss_coverage == 999:
sdss_coverage_flag = "null"
elif sdss_coverage == True:
sdss_coverage_flag = 1
elif sdss_coverage == False:
sdss_coverage_flag = 0
else:
self.log.error('cound not get sdss coverage' % locals())
sys.exit(0)
# UPDATE THE DATABASE FLAG
sqlQuery = u"""
update %(tableName)s set sdss_coverage = %(sdss_coverage_flag)s where primaryID = %(primaryID)s
""" % locals()
writequery(
log=self.log,
sqlQuery=sqlQuery,
dbConn=self.cataloguesDbConn,
)
self.log.debug('completed the ``_update_sdss_coverage`` method')
return None | [
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- check sublime snippet exists
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emichael/PyREM | pyrem/host.py | RemoteHost.run | def run(self, command, **kwargs):
"""Run a command on the remote host.
This is just a wrapper around ``RemoteTask(self.hostname, ...)``
"""
return RemoteTask(self.hostname, command,
identity_file=self._identity_file, **kwargs) | python | def run(self, command, **kwargs):
"""Run a command on the remote host.
This is just a wrapper around ``RemoteTask(self.hostname, ...)``
"""
return RemoteTask(self.hostname, command,
identity_file=self._identity_file, **kwargs) | [
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emichael/PyREM | pyrem/host.py | RemoteHost._rsync_cmd | def _rsync_cmd(self):
"""Helper method to generate base rsync command."""
cmd = ['rsync']
if self._identity_file:
cmd += ['-e', 'ssh -i ' + os.path.expanduser(self._identity_file)]
return cmd | python | def _rsync_cmd(self):
"""Helper method to generate base rsync command."""
cmd = ['rsync']
if self._identity_file:
cmd += ['-e', 'ssh -i ' + os.path.expanduser(self._identity_file)]
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emichael/PyREM | pyrem/host.py | RemoteHost.send_file | def send_file(self, file_name, remote_destination=None, **kwargs):
"""Send a file to a remote host with rsync.
Args:
file_name (str): The relative location of the file on the local
host.
remote_destination (str): The destination for the file on the remote
host. If `None`, will be assumed to be the same as
**file_name**. Default `None`.
**kwargs: Passed to ``SubprocessTask``'s init method.
Return:
``pyrem.task.SubprocessTask``: The resulting task.
"""
if not remote_destination:
remote_destination = file_name
return SubprocessTask(
self._rsync_cmd() +
['-ut', file_name, '%s:%s' % (self.hostname, remote_destination)],
**kwargs) | python | def send_file(self, file_name, remote_destination=None, **kwargs):
"""Send a file to a remote host with rsync.
Args:
file_name (str): The relative location of the file on the local
host.
remote_destination (str): The destination for the file on the remote
host. If `None`, will be assumed to be the same as
**file_name**. Default `None`.
**kwargs: Passed to ``SubprocessTask``'s init method.
Return:
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"""
if not remote_destination:
remote_destination = file_name
return SubprocessTask(
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emichael/PyREM | pyrem/host.py | RemoteHost.get_file | def get_file(self, file_name, local_destination=None, **kwargs):
"""Get a file from a remote host with rsync.
Args:
file_name (str): The relative location of the file on the remote
host.
local_destination (str): The destination for the file on the local
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if not local_destination:
local_destination = file_name
return SubprocessTask(
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**kwargs) | python | def get_file(self, file_name, local_destination=None, **kwargs):
"""Get a file from a remote host with rsync.
Args:
file_name (str): The relative location of the file on the remote
host.
local_destination (str): The destination for the file on the local
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Clinical-Genomics/trailblazer | trailblazer/mip/config.py | ConfigHandler.make_config | def make_config(self, data: dict):
"""Make a MIP config."""
self.validate_config(data)
config_data = self.prepare_config(data)
return config_data | python | def make_config(self, data: dict):
"""Make a MIP config."""
self.validate_config(data)
config_data = self.prepare_config(data)
return config_data | [
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Clinical-Genomics/trailblazer | trailblazer/mip/config.py | ConfigHandler.validate_config | def validate_config(data: dict) -> dict:
"""Convert to MIP config format."""
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if errors:
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for level, sample_errors in messages.items():
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else:
LOG.error(f"{field}: {', '.join(messages)}")
raise ConfigError('invalid config input', errors=errors) | python | def validate_config(data: dict) -> dict:
"""Convert to MIP config format."""
errors = ConfigSchema().validate(data)
if errors:
for field, messages in errors.items():
if isinstance(messages, dict):
for level, sample_errors in messages.items():
sample_id = data['samples'][level]['sample_id']
for sub_field, sub_messages in sample_errors.items():
LOG.error(f"{sample_id} -> {sub_field}: {', '.join(sub_messages)}")
else:
LOG.error(f"{field}: {', '.join(messages)}")
raise ConfigError('invalid config input', errors=errors) | [
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Clinical-Genomics/trailblazer | trailblazer/mip/config.py | ConfigHandler.prepare_config | def prepare_config(data: dict) -> dict:
"""Prepare the config data."""
data_copy = deepcopy(data)
# handle single sample cases with 'unknown' phenotype
if len(data_copy['samples']) == 1:
if data_copy['samples'][0]['phenotype'] == 'unknown':
LOG.info("setting 'unknown' phenotype to 'unaffected'")
data_copy['samples'][0]['phenotype'] = 'unaffected'
# set the mother/father to '0' if they are not set for a sample
for sample_data in data_copy['samples']:
sample_data['mother'] = sample_data.get('mother') or '0'
sample_data['father'] = sample_data.get('father') or '0'
if sample_data['analysis_type'] == 'wgs' and sample_data.get('capture_kit') is None:
sample_data['capture_kit'] = DEFAULT_CAPTURE_KIT
return data_copy | python | def prepare_config(data: dict) -> dict:
"""Prepare the config data."""
data_copy = deepcopy(data)
# handle single sample cases with 'unknown' phenotype
if len(data_copy['samples']) == 1:
if data_copy['samples'][0]['phenotype'] == 'unknown':
LOG.info("setting 'unknown' phenotype to 'unaffected'")
data_copy['samples'][0]['phenotype'] = 'unaffected'
# set the mother/father to '0' if they are not set for a sample
for sample_data in data_copy['samples']:
sample_data['mother'] = sample_data.get('mother') or '0'
sample_data['father'] = sample_data.get('father') or '0'
if sample_data['analysis_type'] == 'wgs' and sample_data.get('capture_kit') is None:
sample_data['capture_kit'] = DEFAULT_CAPTURE_KIT
return data_copy | [
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Clinical-Genomics/trailblazer | trailblazer/mip/config.py | ConfigHandler.save_config | def save_config(self, data: dict) -> Path:
"""Save a config to the expected location."""
out_dir = Path(self.families_dir) / data['family']
out_dir.mkdir(parents=True, exist_ok=True)
out_path = out_dir / 'pedigree.yaml'
dump = ruamel.yaml.round_trip_dump(data, indent=4, block_seq_indent=2)
out_path.write_text(dump)
return out_path | python | def save_config(self, data: dict) -> Path:
"""Save a config to the expected location."""
out_dir = Path(self.families_dir) / data['family']
out_dir.mkdir(parents=True, exist_ok=True)
out_path = out_dir / 'pedigree.yaml'
dump = ruamel.yaml.round_trip_dump(data, indent=4, block_seq_indent=2)
out_path.write_text(dump)
return out_path | [
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andrewda/frc-livescore | livescore/simpleocr_utils/processor.py | _broadcast | def _broadcast(src_processor, src_atr_name, dest_processors, dest_atr_name, transform_function):
"""
To be used exclusively by create_broadcast.
A broadcast function gets an attribute on the src_processor and
sets it (possibly under a different name) on dest_processors
"""
value = getattr(src_processor, src_atr_name)
value = transform_function(value)
for d in dest_processors:
setattr(d, dest_atr_name, value) | python | def _broadcast(src_processor, src_atr_name, dest_processors, dest_atr_name, transform_function):
"""
To be used exclusively by create_broadcast.
A broadcast function gets an attribute on the src_processor and
sets it (possibly under a different name) on dest_processors
"""
value = getattr(src_processor, src_atr_name)
value = transform_function(value)
for d in dest_processors:
setattr(d, dest_atr_name, value) | [
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andrewda/frc-livescore | livescore/simpleocr_utils/processor.py | create_broadcast | def create_broadcast(src_atr_name, dest_processors, dest_atr_name=None, transform_function=lambda x: x):
"""
This method creates a function, intended to be called as a
Processor posthook, that copies some of the processor's attributes
to other processors
"""
from functools import partial
if dest_atr_name == None:
dest_atr_name = src_atr_name
if not hasattr(dest_processors, "__iter__"): # a single processor was given instead
dest_processors = [dest_processors]
return partial(_broadcast, src_atr_name=src_atr_name, dest_processors=dest_processors, dest_atr_name=dest_atr_name,
transform_function=transform_function) | python | def create_broadcast(src_atr_name, dest_processors, dest_atr_name=None, transform_function=lambda x: x):
"""
This method creates a function, intended to be called as a
Processor posthook, that copies some of the processor's attributes
to other processors
"""
from functools import partial
if dest_atr_name == None:
dest_atr_name = src_atr_name
if not hasattr(dest_processors, "__iter__"): # a single processor was given instead
dest_processors = [dest_processors]
return partial(_broadcast, src_atr_name=src_atr_name, dest_processors=dest_processors, dest_atr_name=dest_atr_name,
transform_function=transform_function) | [
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andrewda/frc-livescore | livescore/simpleocr_utils/processor.py | Processor.get_parameters | def get_parameters(self):
"""returns a dictionary with the processor's stored parameters"""
parameter_names = self.PARAMETERS.keys()
# TODO: Unresolved reference for processor
parameter_values = [getattr(processor, n) for n in parameter_names]
return dict(zip(parameter_names, parameter_values)) | python | def get_parameters(self):
"""returns a dictionary with the processor's stored parameters"""
parameter_names = self.PARAMETERS.keys()
# TODO: Unresolved reference for processor
parameter_values = [getattr(processor, n) for n in parameter_names]
return dict(zip(parameter_names, parameter_values)) | [
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andrewda/frc-livescore | livescore/simpleocr_utils/processor.py | Processor.set_parameters | def set_parameters(self, **args):
"""sets the processor stored parameters"""
for k, v in self.PARAMETERS.items():
new_value = args.get(k)
if new_value != None:
if not _same_type(new_value, v):
raise Exception(
"On processor {0}, argument {1} takes something like {2}, but {3} was given".format(self, k, v,
new_value))
setattr(self, k, new_value)
not_used = set(args.keys()).difference(set(self.PARAMETERS.keys()))
not_given = set(self.PARAMETERS.keys()).difference(set(args.keys()))
return not_used, not_given | python | def set_parameters(self, **args):
"""sets the processor stored parameters"""
for k, v in self.PARAMETERS.items():
new_value = args.get(k)
if new_value != None:
if not _same_type(new_value, v):
raise Exception(
"On processor {0}, argument {1} takes something like {2}, but {3} was given".format(self, k, v,
new_value))
setattr(self, k, new_value)
not_used = set(args.keys()).difference(set(self.PARAMETERS.keys()))
not_given = set(self.PARAMETERS.keys()).difference(set(args.keys()))
return not_used, not_given | [
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andrewda/frc-livescore | livescore/simpleocr_utils/processor.py | ProcessorStack.get_parameters | def get_parameters(self):
"""gets from all wrapped processors"""
d = {}
for p in self.processors:
parameter_names = list(p.PARAMETERS.keys())
parameter_values = [getattr(p, n) for n in parameter_names]
d.update(dict(zip(parameter_names, parameter_values)))
return d | python | def get_parameters(self):
"""gets from all wrapped processors"""
d = {}
for p in self.processors:
parameter_names = list(p.PARAMETERS.keys())
parameter_values = [getattr(p, n) for n in parameter_names]
d.update(dict(zip(parameter_names, parameter_values)))
return d | [
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