Datasets:
Denis641
/
AdvTestNegatives

Dataset card Data Studio Files
xet
Community
1
query
stringlengths
5
1.23k
positive
stringlengths
53
15.2k
id_
int64
0
252k
task_name
stringlengths
87
242
negative
listlengths
20
553
generate one Schlumberger sounding configuration that is one set of configurations for one potential dipole MN .
def gen_schlumberger ( self , M , N , a = None ) : if a is None : a = np . abs ( M - N ) nr_of_steps_left = int ( min ( M , N ) - 1 / a ) nr_of_steps_right = int ( ( self . nr_electrodes - max ( M , N ) ) / a ) configs = [ ] for i in range ( 0 , min ( nr_of_steps_left , nr_of_steps_right ) ) : A = min ( M , N ) - ( i + 1 ) * a B = max ( M , N ) + ( i + 1 ) * a configs . append ( ( A , B , M , N ) ) configs = np . array ( configs ) self . add_to_configs ( configs ) return configs
8,400
https://github.com/geophysics-ubonn/reda/blob/46a939729e40c7c4723315c03679c40761152e9e/lib/reda/configs/configManager.py#L459-L498
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Add one or more measurement configurations to the stored configurations
def add_to_configs ( self , configs ) : if len ( configs ) == 0 : return None if self . configs is None : self . configs = np . atleast_2d ( configs ) else : configs = np . atleast_2d ( configs ) self . configs = np . vstack ( ( self . configs , configs ) ) return self . configs
8,401
https://github.com/geophysics-ubonn/reda/blob/46a939729e40c7c4723315c03679c40761152e9e/lib/reda/configs/configManager.py#L521-L543
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Split the stored configurations into normal and reciprocal measurements
def split_into_normal_and_reciprocal ( self , pad = False , return_indices = False ) : # for simplicity, we create an array where AB and MN are sorted configs = np . hstack ( ( np . sort ( self . configs [ : , 0 : 2 ] , axis = 1 ) , np . sort ( self . configs [ : , 2 : 4 ] , axis = 1 ) ) ) ab_min = configs [ : , 0 ] mn_min = configs [ : , 2 ] # rule 1 indices_normal = np . where ( ab_min < mn_min ) [ 0 ] # now look for reciprocals indices_used = [ ] normal = [ ] normal_indices = [ ] reciprocal_indices = [ ] reciprocal = [ ] duplicates = [ ] for index in indices_normal : indices_used . append ( index ) normal . append ( self . configs [ index , : ] ) normal_indices . append ( index ) # look for reciprocal configuration index_rec = np . where ( # A == M, B == N, M == A, N == B ( configs [ : , 0 ] == configs [ index , 2 ] ) & ( configs [ : , 1 ] == configs [ index , 3 ] ) & ( configs [ : , 2 ] == configs [ index , 0 ] ) & ( configs [ : , 3 ] == configs [ index , 1 ] ) ) [ 0 ] if len ( index_rec ) == 0 and pad : reciprocal . append ( np . ones ( 4 ) * np . nan ) elif len ( index_rec ) == 1 : reciprocal . append ( self . configs [ index_rec [ 0 ] , : ] ) indices_used . append ( index_rec [ 0 ] ) reciprocal_indices . append ( index_rec [ 0 ] ) elif len ( index_rec > 1 ) : # take the first one reciprocal . append ( self . configs [ index_rec [ 0 ] , : ] ) reciprocal_indices . append ( index_rec [ 0 ] ) duplicates += list ( index_rec [ 1 : ] ) indices_used += list ( index_rec ) # now determine all reciprocal-only parameters set_all_indices = set ( list ( range ( 0 , configs . shape [ 0 ] ) ) ) set_used_indices = set ( indices_used ) reciprocal_only_indices = set_all_indices - set_used_indices for index in reciprocal_only_indices : if pad : normal . append ( np . ones ( 4 ) * np . nan ) reciprocal . append ( self . configs [ index , : ] ) normals = np . array ( normal ) reciprocals = np . array ( reciprocal ) if return_indices : return normals , reciprocals , normal_indices , reciprocal_indices else : return normals , reciprocals
8,402
https://github.com/geophysics-ubonn/reda/blob/46a939729e40c7c4723315c03679c40761152e9e/lib/reda/configs/configManager.py#L545-L638
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Generate reciprocal configurations sort by AB and optionally append to configurations .
def gen_reciprocals ( self , append = False ) : # Switch AB and MN reciprocals = self . configs . copy ( ) [ : , : : - 1 ] reciprocals [ : , 0 : 2 ] = np . sort ( reciprocals [ : , 0 : 2 ] , axis = 1 ) reciprocals [ : , 2 : 4 ] = np . sort ( reciprocals [ : , 2 : 4 ] , axis = 1 ) # # Sort by current dipoles ind = np . lexsort ( ( reciprocals [ : , 3 ] , reciprocals [ : , 2 ] , reciprocals [ : , 1 ] , reciprocals [ : , 0 ] ) ) reciprocals = reciprocals [ ind ] if append : self . configs = np . vstack ( ( self . configs , reciprocals ) ) return reciprocals
8,403
https://github.com/geophysics-ubonn/reda/blob/46a939729e40c7c4723315c03679c40761152e9e/lib/reda/configs/configManager.py#L640-L673
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Create measurement configurations out of a pool of current injections . Use only the provided dipoles for potential dipole selection . This means that we have always reciprocal measurements .
def gen_configs_permutate ( self , injections_raw , only_same_dipole_length = False , ignore_crossed_dipoles = False , silent = False ) : injections = np . atleast_2d ( injections_raw ) . astype ( int ) N = injections . shape [ 0 ] measurements = [ ] for injection in range ( 0 , N ) : dipole_length = np . abs ( injections [ injection ] [ 1 ] - injections [ injection ] [ 0 ] ) # select all dipole EXCEPT for the injection dipole for i in set ( range ( 0 , N ) ) - set ( [ injection ] ) : test_dipole_length = np . abs ( injections [ i , : ] [ 1 ] - injections [ i , : ] [ 0 ] ) if ( only_same_dipole_length and test_dipole_length != dipole_length ) : continue quadpole = np . array ( [ injections [ injection , : ] , injections [ i , : ] ] ) . flatten ( ) if ignore_crossed_dipoles is True : # check if we need to ignore this dipole # Note: this could be wrong if electrode number are not # ascending! if ( quadpole [ 2 ] > quadpole [ 0 ] and quadpole [ 2 ] < quadpole [ 1 ] ) : if not silent : print ( 'A - ignoring' , quadpole ) elif ( quadpole [ 3 ] > quadpole [ 0 ] and quadpole [ 3 ] < quadpole [ 1 ] ) : if not silent : print ( 'B - ignoring' , quadpole ) else : measurements . append ( quadpole ) else : # add very quadpole measurements . append ( quadpole ) # check and remove double use of electrodes filtered = [ ] for quadpole in measurements : if ( not set ( quadpole [ 0 : 2 ] ) . isdisjoint ( set ( quadpole [ 2 : 4 ] ) ) ) : if not silent : print ( 'Ignoring quadrupole because of ' , 'repeated electrode use:' , quadpole ) else : filtered . append ( quadpole ) self . add_to_configs ( filtered ) return np . array ( filtered )
8,404
https://github.com/geophysics-ubonn/reda/blob/46a939729e40c7c4723315c03679c40761152e9e/lib/reda/configs/configManager.py#L675-L753
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Remove configurations with dipole separations higher than maxsep .
def remove_max_dipole_sep ( self , maxsep = 10 ) : sep = np . abs ( self . configs [ : , 1 ] - self . configs [ : , 2 ] ) self . configs = self . configs [ sep <= maxsep ]
8,405
https://github.com/geophysics-ubonn/reda/blob/46a939729e40c7c4723315c03679c40761152e9e/lib/reda/configs/configManager.py#L755-L764
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Convert the configuration to a pygimli measurement scheme
def to_pg_scheme ( self , container = None , positions = None ) : if container is None and positions is None : raise Exception ( 'electrode positions are required for BERT export' ) if container is not None and container . electrodes is None : raise Exception ( 'container does not contain electrode positions' ) if container is not None and positions is not None : raise Exception ( 'only one of container OR positions must be provided' ) if container is not None : elec_positions = container . electrodes . values elif positions is not None : elec_positions = positions opt_import ( "pybert" , requiredFor = "" ) import pybert # Initialize BERT DataContainer data = pybert . DataContainerERT ( ) # Define electrodes (48 electrodes spaced by 0.5 m) for nr , ( x , y , z ) in enumerate ( elec_positions ) : data . createSensor ( ( x , y , z ) ) # Define number of measurements data . resize ( self . configs . shape [ 0 ] ) for index , token in enumerate ( "abmn" ) : data . set ( token , self . configs [ : , index ] . tolist ( ) ) # account for zero indexing for token in "abmn" : data . set ( token , data ( token ) - 1 ) # np.vstack([data.get(x).array() for x in ("abmn")]).T return data
8,406
https://github.com/geophysics-ubonn/reda/blob/46a939729e40c7c4723315c03679c40761152e9e/lib/reda/configs/configManager.py#L771-L836
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Export to IRIS Instrument configuration file
def to_iris_syscal ( self , filename ) : with open ( filename , 'w' ) as fid : # fprintf(fod, '#\t X\t Y\t Z\n'); fid . write ( '#\t X\t Y\t Z\n' ) # fprintf(fod, '%d\t %.1f\t %d\t %d\n', D'); # loop over electrodes and assign increasing x-positions # TODO: use proper electrode positions, if available for nr in range ( 0 , self . configs . max ( ) ) : fid . write ( '{} {} 0 0\n' . format ( nr + 1 , nr ) ) # fprintf(fod, '#\t A\t B\t M\t N\n'); fid . write ( '#\t A\t B\t M\t N\n' ) # fprintf(fod, '%d\t %d\t %d\t %d\t %d\n', C'); for nr , config in enumerate ( self . configs ) : fid . write ( '{} {} {} {} {}\n' . format ( nr + 1 , * config ) )
8,407
https://github.com/geophysics-ubonn/reda/blob/46a939729e40c7c4723315c03679c40761152e9e/lib/reda/configs/configManager.py#L838-L860
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Creating a new plan for subscriptions associated with the merchant .
def create_plan ( self , * , plan_code , description , interval , interval_count , max_payments_allowed , payment_attempts_delay , plan_value , plan_tax , plan_tax_return_base , currency , max_payment_attempts = None , max_pending_payments = None , trial_days = None ) : payload = { "accountId" : self . client . account_id , "planCode" : plan_code , "description" : description , "interval" : interval , "intervalCount" : interval_count , "maxPaymentsAllowed" : max_payments_allowed , "paymentAttemptsDelay" : payment_attempts_delay , "additionalValues" : [ { "name" : "PLAN_VALUE" , "value" : plan_value , "currency" : currency } , { "name" : "PLAN_TAX" , "value" : plan_tax , "currency" : currency } , { "name" : "PLAN_TAX_RETURN_BASE" , "value" : plan_tax_return_base , "currency" : currency } ] , "maxPaymentAttempts" : max_payment_attempts , "maxPendingPayments" : max_pending_payments , "trialDays" : trial_days } return self . client . _post ( self . url + 'plans' , json = payload , headers = self . get_headers ( ) )
8,408
https://github.com/GearPlug/payu-python/blob/47ec5c9fc89f1f89a53ec0a68c84f358bbe3394e/payu/recurring.py#L10-L90
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Check all the information of a plan for subscriptions associated with the merchant .
def get_plan ( self , plan_code ) : return self . client . _get ( self . url + 'plans/{}' . format ( plan_code ) , headers = self . get_headers ( ) )
8,409
https://github.com/GearPlug/payu-python/blob/47ec5c9fc89f1f89a53ec0a68c84f358bbe3394e/payu/recurring.py#L92-L102
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Delete an entire subscription plan associated with the merchant .
def delete_plan ( self , plan_code ) : return self . client . _delete ( self . url + 'plans/{}' . format ( plan_code ) , headers = self . get_headers ( ) )
8,410
https://github.com/GearPlug/payu-python/blob/47ec5c9fc89f1f89a53ec0a68c84f358bbe3394e/payu/recurring.py#L107-L117
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Creation of a customer in the system .
def create_customer ( self , * , full_name , email ) : payload = { "fullName" : full_name , "email" : email } return self . client . _post ( self . url + 'customers' , json = payload , headers = self . get_headers ( ) )
8,411
https://github.com/GearPlug/payu-python/blob/47ec5c9fc89f1f89a53ec0a68c84f358bbe3394e/payu/recurring.py#L119-L137
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Queries the information related to the customer .
def get_customer ( self , customer_id ) : return self . client . _get ( self . url + 'customers/{}' . format ( customer_id ) , headers = self . get_headers ( ) )
8,412
https://github.com/GearPlug/payu-python/blob/47ec5c9fc89f1f89a53ec0a68c84f358bbe3394e/payu/recurring.py#L139-L149
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Removes a user from the system .
def delete_customer ( self , customer_id ) : return self . client . _delete ( self . url + 'customers/{}' . format ( customer_id ) , headers = self . get_headers ( ) )
8,413
https://github.com/GearPlug/payu-python/blob/47ec5c9fc89f1f89a53ec0a68c84f358bbe3394e/payu/recurring.py#L154-L164
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Creating a new subscription of a client to a plan .
def create_subscription ( self , * , customer_id , credit_card_token , plan_code , quantity = None , installments = None , trial_days = None , immediate_payment = None , extra1 = None , extra2 = None , delivery_address = None , notify_url = None , recurring_bill_items = None ) : payload = { "quantity" : quantity , "installments" : installments , "trialDays" : trial_days , "immediatePayment" : immediate_payment , "extra1" : extra1 , "extra2" : extra2 , "customer" : { "id" : customer_id , "creditCards" : [ { "token" : credit_card_token } ] } , "plan" : { "planCode" : plan_code } , "deliveryAddress" : delivery_address , "notifyUrl" : notify_url , "recurringBillItems" : recurring_bill_items } return self . client . _post ( self . url + 'subscriptions' , json = payload , headers = self . get_headers ( ) )
8,414
https://github.com/GearPlug/payu-python/blob/47ec5c9fc89f1f89a53ec0a68c84f358bbe3394e/payu/recurring.py#L240-L303
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Check the basic information associated with the specified subscription .
def get_subscription ( self , subscription_id ) : return self . client . _put ( self . url + 'subscriptions/{}' . format ( subscription_id ) , headers = self . get_headers ( ) )
8,415
https://github.com/GearPlug/payu-python/blob/47ec5c9fc89f1f89a53ec0a68c84f358bbe3394e/payu/recurring.py#L305-L315
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Update information associated with the specified subscription . At the moment it is only possible to update the token of the credit card to which the charge of the subscription is made .
def update_subscription ( self , * , subscription_id , credit_card_token ) : payload = { "creditCardToken" : credit_card_token } fmt = 'subscriptions/{}' . format ( subscription_id ) return self . client . _put ( self . url + fmt , json = payload , headers = self . get_headers ( ) )
8,416
https://github.com/GearPlug/payu-python/blob/47ec5c9fc89f1f89a53ec0a68c84f358bbe3394e/payu/recurring.py#L317-L333
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Unsubscribe delete the relationship of the customer with the plan .
def delete_subscription ( self , subscription_id ) : return self . client . _delete ( self . url + 'subscriptions/{}' . format ( subscription_id ) , headers = self . get_headers ( ) )
8,417
https://github.com/GearPlug/payu-python/blob/47ec5c9fc89f1f89a53ec0a68c84f358bbe3394e/payu/recurring.py#L335-L345
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Adds extra charges to the respective invoice for the current period .
def create_additional_charge ( self , * , subscription_id , description , plan_value , plan_tax , plan_tax_return_base , currency ) : payload = { "description" : description , "additionalValues" : [ { "name" : "ITEM_VALUE" , "value" : plan_value , "currency" : currency } , { "name" : "ITEM_TAX" , "value" : plan_tax , "currency" : currency } , { "name" : "ITEM_TAX_RETURN_BASE" , "value" : plan_tax_return_base , "currency" : currency } ] } fmt = 'subscriptions/{}/recurringBillItems' . format ( subscription_id ) return self . client . _post ( self . url + fmt , json = payload , headers = self . get_headers ( ) )
8,418
https://github.com/GearPlug/payu-python/blob/47ec5c9fc89f1f89a53ec0a68c84f358bbe3394e/payu/recurring.py#L347-L384
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Query extra charge information of an invoice from its identifier .
def get_additional_charge_by_identifier ( self , recurring_billing_id ) : fmt = 'recurringBillItems/{}' . format ( recurring_billing_id ) return self . client . _get ( self . url + fmt , headers = self . get_headers ( ) )
8,419
https://github.com/GearPlug/payu-python/blob/47ec5c9fc89f1f89a53ec0a68c84f358bbe3394e/payu/recurring.py#L386-L397
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Updates the information from an additional charge in an invoice .
def update_additional_charge ( self , * , recurring_billing_id , description , plan_value , plan_tax , plan_tax_return_base , currency ) : payload = { "description" : description , "additionalValues" : [ { "name" : "ITEM_VALUE" , "value" : plan_value , "currency" : currency } , { "name" : "ITEM_TAX" , "value" : plan_tax , "currency" : currency } , { "name" : "ITEM_TAX_RETURN_BASE" , "value" : plan_tax_return_base , "currency" : currency } ] } fmt = 'recurringBillItems/{}' . format ( recurring_billing_id ) return self . client . _put ( self . url + fmt , payload = payload , headers = self . get_headers ( ) )
8,420
https://github.com/GearPlug/payu-python/blob/47ec5c9fc89f1f89a53ec0a68c84f358bbe3394e/payu/recurring.py#L429-L466
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Remove an extra charge from an invoice .
def delete_additional_charge ( self , recurring_billing_id ) : fmt = 'recurringBillItems/{}' . format ( recurring_billing_id ) return self . client . _delete ( self . url + fmt , headers = self . get_headers ( ) )
8,421
https://github.com/GearPlug/payu-python/blob/47ec5c9fc89f1f89a53ec0a68c84f358bbe3394e/payu/recurring.py#L468-L479
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Creates a thumbnail of for an ImageField .
def thumbnail ( parser , token ) : args = token . split_contents ( ) tag = args [ 0 ] # Check to see if we're setting to a context variable. if len ( args ) > 4 and args [ - 2 ] == 'as' : context_name = args [ - 1 ] args = args [ : - 2 ] else : context_name = None if len ( args ) < 3 : raise TemplateSyntaxError ( "Invalid syntax. Expected " "'{%% %s source size [option1 option2 ...] %%}' or " "'{%% %s source size [option1 option2 ...] as variable %%}'" % ( tag , tag ) ) # Get the source image path and requested size. source_var = args [ 1 ] # If the size argument was a correct static format, wrap it in quotes so # that it is compiled correctly. m = REGEXP_THUMB_SIZES . match ( args [ 2 ] ) if m : args [ 2 ] = '"%s"' % args [ 2 ] size_var = args [ 2 ] # Get the options. args_list = split_args ( args [ 3 : ] ) . items ( ) # Check the options. opts = { } kwargs = { } # key,values here override settings and defaults for arg , value in args_list : value = value and parser . compile_filter ( value ) if arg in TAG_SETTINGS and value is not None : kwargs [ str ( arg ) ] = value continue else : raise TemplateSyntaxError ( "'%s' tag received a bad argument: " "'%s'" % ( tag , arg ) ) return ThumbnailNode ( source_var , size_var , opts = opts , context_name = context_name , * * kwargs )
8,422
https://github.com/gtaylor/django-athumb/blob/69261ace0dff81e33156a54440874456a7b38dfb/athumb/templatetags/thumbnail.py#L142-L201
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Print the requested statistics values for those fields specified on input .
def printStats ( self ) : print ( "--- Imagestats Results ---" ) if ( self . fields . find ( 'npix' ) != - 1 ) : print ( "Number of pixels : " , self . npix ) if ( self . fields . find ( 'min' ) != - 1 ) : print ( "Minimum value : " , self . min ) if ( self . fields . find ( 'max' ) != - 1 ) : print ( "Maximum value : " , self . max ) if ( self . fields . find ( 'stddev' ) != - 1 ) : print ( "Standard Deviation: " , self . stddev ) if ( self . fields . find ( 'mean' ) != - 1 ) : print ( "Mean : " , self . mean ) if ( self . fields . find ( 'mode' ) != - 1 ) : print ( "Mode : " , self . mode ) if ( self . fields . find ( 'median' ) != - 1 ) : print ( "Median : " , self . median ) if ( self . fields . find ( 'midpt' ) != - 1 ) : print ( "Midpt : " , self . midpt )
8,423
https://github.com/spacetelescope/stsci.imagestats/blob/d7fc9fe9783f7ed3dc9e4af47acd357a5ccd68e3/stsci/imagestats/__init__.py#L332-L351
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Perform a WVA web services request and return the raw response object
def raw_request ( self , method , uri , * * kwargs ) : with warnings . catch_warnings ( ) : # catch warning about certs not being verified warnings . simplefilter ( "ignore" , urllib3 . exceptions . InsecureRequestWarning ) warnings . simplefilter ( "ignore" , urllib3 . exceptions . InsecurePlatformWarning ) try : response = self . _get_session ( ) . request ( method , self . _get_ws_url ( uri ) , * * kwargs ) except requests . RequestException as e : # e.g. raise new_exc from old_exc six . raise_from ( WVAHttpRequestError ( e ) , e ) else : return response
8,424
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/http_client.py#L79-L97
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Perform a WVA web services request and return the decoded value if successful
def request ( self , method , uri , * * kwargs ) : response = self . raw_request ( method , uri , * * kwargs ) if response . status_code != 200 : exception_class = HTTP_STATUS_EXCEPTION_MAP . get ( response . status_code , WVAHttpError ) raise exception_class ( response ) if response . headers . get ( "content-type" ) == "application/json" : return json . loads ( response . text ) else : return response . text
8,425
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/http_client.py#L99-L121
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POST the provided data to the specified path
def post ( self , uri , data , * * kwargs ) : return self . request ( "POST" , uri , data = data , * * kwargs )
8,426
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/http_client.py#L137-L143
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POST the provided data as json to the specified path
def post_json ( self , uri , data , * * kwargs ) : encoded_data = json . dumps ( data ) kwargs . setdefault ( "headers" , { } ) . update ( { "Content-Type" : "application/json" , # tell server we are sending json } ) return self . post ( uri , data = encoded_data , * * kwargs )
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PUT the provided data to the specified path
def put ( self , uri , data , * * kwargs ) : return self . request ( "PUT" , uri , data = data , * * kwargs )
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PUT the provided data as json to the specified path
def put_json ( self , uri , data , * * kwargs ) : encoded_data = json . dumps ( data ) kwargs . setdefault ( "headers" , { } ) . update ( { "Content-Type" : "application/json" , # tell server we are sending json } ) return self . put ( uri , data = encoded_data , * * kwargs )
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[ "def", "state_histogram", "(", "rho", ",", "ax", "=", "None", ",", "title", "=", "\"\"", ",", "threshold", "=", "0.001", ")", ":", "rho_amps", "=", "rho", ".", "data", ".", "toarray", "(", ")", ".", "ravel", "(", ")", "nqc", "=", "int", "(", "round", "(", "np", ".", "log2", "(", "rho", ".", "shape", "[", "0", "]", ")", ")", ")", "if", "ax", "is", "None", ":", "fig", "=", "plt", ".", "figure", "(", "figsize", "=", "(", "10", ",", "6", ")", ")", "ax", "=", "Axes3D", "(", "fig", ",", "azim", "=", "-", "35", ",", "elev", "=", "35", ")", "cmap", "=", "rigetti_4_color_cm", "norm", "=", "mpl", ".", "colors", ".", "Normalize", "(", "-", "np", ".", "pi", ",", "np", ".", "pi", ")", "colors", "=", "cmap", "(", "norm", "(", "np", ".", "angle", "(", "rho_amps", ")", ")", ")", "dzs", "=", "abs", "(", "rho_amps", ")", "colors", "[", ":", ",", "3", "]", "=", "1.0", "*", "(", "dzs", ">", "threshold", ")", "xs", ",", "ys", "=", "np", ".", "meshgrid", "(", "range", "(", "2", "**", "nqc", ")", ",", "range", "(", "2", "**", "nqc", ")", ")", "xs", "=", "xs", ".", "ravel", "(", ")", "ys", "=", "ys", ".", "ravel", "(", ")", "zs", "=", "np", ".", "zeros_like", "(", "xs", ")", "dxs", "=", "dys", "=", "np", ".", "ones_like", "(", "xs", ")", "*", "0.8", "_", "=", "ax", ".", "bar3d", "(", "xs", ",", "ys", ",", "zs", ",", "dxs", ",", "dys", ",", "dzs", ",", "color", "=", "colors", ")", "ax", ".", "set_xticks", "(", "np", ".", "arange", "(", "2", "**", "nqc", ")", "+", ".4", ")", "ax", ".", "set_xticklabels", "(", "basis_labels", "(", "nqc", ")", ")", "ax", ".", "set_yticks", "(", "np", ".", "arange", "(", "2", "**", "nqc", ")", "+", ".4", ")", "ax", ".", "set_yticklabels", "(", "basis_labels", "(", "nqc", ")", ")", "ax", ".", "set_zlim3d", "(", "[", "0", ",", "1", "]", ")", "cax", ",", "kw", "=", "mpl", ".", "colorbar", ".", "make_axes", "(", "ax", ",", "shrink", "=", ".75", ",", "pad", "=", ".1", ")", "cb", "=", "mpl", ".", "colorbar", ".", "ColorbarBase", "(", "cax", ",", "cmap", "=", "cmap", ",", "norm", "=", "norm", ")", "cb", ".", "set_ticks", "(", "[", "-", "np", ".", "pi", ",", "-", "np", ".", "pi", "/", "2", ",", "0", ",", "np", ".", "pi", "/", "2", ",", "np", ".", "pi", "]", ")", "cb", ".", "set_ticklabels", "(", "(", "r'$-\\pi$'", ",", "r'$-\\pi/2$'", ",", "r'$0$'", ",", "r'$\\pi/2$'", ",", "r'$\\pi$'", ")", ")", "cb", ".", "set_label", "(", "'arg'", ")", "ax", ".", "view_init", "(", "azim", "=", "-", "55", ",", "elev", "=", "45", ")", "ax", ".", "set_title", "(", "title", ")", "return", "ax" ]
Translate a MAC address into an IPv6 address in the prefixed network .
def mac_to_ipv6_linklocal ( mac , prefix = "fe80::" ) : # Remove the most common delimiters; dots, dashes, etc. mac_value = int ( mac . translate ( str . maketrans ( dict ( [ ( x , None ) for x in [ " " , "." , ":" , "-" ] ] ) ) ) , 16 ) # Split out the bytes that slot into the IPv6 address # XOR the most significant byte with 0x02, inverting the # Universal / Local bit high2 = mac_value >> 32 & 0xffff ^ 0x0200 high1 = mac_value >> 24 & 0xff low1 = mac_value >> 16 & 0xff low2 = mac_value & 0xffff return prefix + ':{:04x}:{:02x}ff:fe{:02x}:{:04x}' . format ( high2 , high1 , low1 , low2 )
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Method run when data is received from the device
def datagram_received ( self , data , addr ) : self . register ( ) response = unpack_lifx_message ( data ) self . lastmsg = datetime . datetime . now ( ) if response . seq_num in self . message : response_type , myevent , callb = self . message [ response . seq_num ] if type ( response ) == response_type : if response . source_id == self . source_id : if "State" in response . __class__ . __name__ : setmethod = "resp_set_" + response . __class__ . __name__ . replace ( "State" , "" ) . lower ( ) if setmethod in dir ( self ) and callable ( getattr ( self , setmethod ) ) : getattr ( self , setmethod ) ( response ) if callb : callb ( self , response ) myevent . set ( ) del ( self . message [ response . seq_num ] ) elif type ( response ) == Acknowledgement : pass else : del ( self . message [ response . seq_num ] ) elif self . default_callb : self . default_callb ( response )
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Proxy method to register the device with the parent .
def register ( self ) : if not self . registered : self . registered = True if self . parent : self . parent . register ( self )
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[ "def", "pages", "(", "self", ")", ":", "# protected access has to be permitted here to not close the paginator's pages", "# pylint: disable=protected-access", "paginator_pages", "=", "list", "(", "self", ".", "paginator", ".", "_pages", ")", "if", "len", "(", "self", ".", "paginator", ".", "_current_page", ")", ">", "1", ":", "paginator_pages", ".", "append", "(", "'\\n'", ".", "join", "(", "self", ".", "paginator", ".", "_current_page", ")", "+", "'\\n'", "+", "(", "self", ".", "paginator", ".", "suffix", "or", "''", ")", ")", "# pylint: enable=protected-access", "return", "paginator_pages" ]
Proxy method to unregister the device with the parent .
def unregister ( self ) : if self . registered : #Only if we have not received any message recently. if datetime . datetime . now ( ) - datetime . timedelta ( seconds = self . unregister_timeout ) > self . lastmsg : self . registered = False if self . parent : self . parent . unregister ( self )
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Coroutine used to send message to the device when no response is needed .
async def fire_sending ( self , msg , num_repeats ) : if num_repeats is None : num_repeats = self . retry_count sent_msg_count = 0 sleep_interval = 0.05 while ( sent_msg_count < num_repeats ) : if self . transport : self . transport . sendto ( msg . packed_message ) sent_msg_count += 1 await aio . sleep ( sleep_interval )
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Coroutine used to send message to the device when a response or ack is needed .
async def try_sending ( self , msg , timeout_secs , max_attempts ) : if timeout_secs is None : timeout_secs = self . timeout if max_attempts is None : max_attempts = self . retry_count attempts = 0 while attempts < max_attempts : if msg . seq_num not in self . message : return event = aio . Event ( ) self . message [ msg . seq_num ] [ 1 ] = event attempts += 1 if self . transport : self . transport . sendto ( msg . packed_message ) try : myresult = await aio . wait_for ( event . wait ( ) , timeout_secs ) break except Exception as inst : if attempts >= max_attempts : if msg . seq_num in self . message : callb = self . message [ msg . seq_num ] [ 2 ] if callb : callb ( self , None ) del ( self . message [ msg . seq_num ] ) #It's dead Jim self . unregister ( )
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Method to send a message expecting to receive an ACK .
def req_with_ack ( self , msg_type , payload , callb = None , timeout_secs = None , max_attempts = None ) : msg = msg_type ( self . mac_addr , self . source_id , seq_num = self . seq_next ( ) , payload = payload , ack_requested = True , response_requested = False ) self . message [ msg . seq_num ] = [ Acknowledgement , None , callb ] xx = self . loop . create_task ( self . try_sending ( msg , timeout_secs , max_attempts ) ) return True
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[ "def", "configure", "(", "self", ",", "organization", ",", "base_url", "=", "''", ",", "ttl", "=", "''", ",", "max_ttl", "=", "''", ",", "mount_point", "=", "DEFAULT_MOUNT_POINT", ")", ":", "params", "=", "{", "'organization'", ":", "organization", ",", "'base_url'", ":", "base_url", ",", "'ttl'", ":", "ttl", ",", "'max_ttl'", ":", "max_ttl", ",", "}", "api_path", "=", "'/v1/auth/{mount_point}/config'", ".", "format", "(", "mount_point", "=", "mount_point", ")", "return", "self", ".", "_adapter", ".", "post", "(", "url", "=", "api_path", ",", "json", "=", "params", ",", ")" ]
Convenience method to request the label from the device
def get_label ( self , callb = None ) : if self . label is None : mypartial = partial ( self . resp_set_label ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) response = self . req_with_resp ( GetLabel , StateLabel , callb = mycallb ) return self . label
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[ "def", "_page_update", "(", "self", ",", "event", ")", ":", "try", ":", "if", "event", ".", "schema", "==", "'wikipage'", ":", "self", ".", "_update_index", "(", ")", "except", "Exception", "as", "e", ":", "self", ".", "log", "(", "\"Page creation notification error: \"", ",", "event", ",", "e", ",", "type", "(", "e", ")", ",", "lvl", "=", "error", ")" ]
Convenience method to set the label of the device
def set_label ( self , value , callb = None ) : if len ( value ) > 32 : value = value [ : 32 ] mypartial = partial ( self . resp_set_label , label = value ) if callb : self . req_with_ack ( SetLabel , { "label" : value } , lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) ) else : self . req_with_ack ( SetLabel , { "label" : value } , lambda x , y : mypartial ( y ) )
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[ "def", "_read_columns_file", "(", "f", ")", ":", "try", ":", "columns", "=", "json", ".", "loads", "(", "open", "(", "f", ",", "'r'", ")", ".", "read", "(", ")", ",", "object_pairs_hook", "=", "collections", ".", "OrderedDict", ")", "except", "Exception", "as", "err", ":", "raise", "InvalidColumnsFileError", "(", "\"There was an error while reading {0}: {1}\"", ".", "format", "(", "f", ",", "err", ")", ")", "# Options are not supported yet:", "if", "'__options'", "in", "columns", ":", "del", "columns", "[", "'__options'", "]", "return", "columns" ]
Convenience method to request the location from the device
def get_location ( self , callb = None ) : if self . location is None : mypartial = partial ( self . resp_set_location ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) response = self . req_with_resp ( GetLocation , StateLocation , callb = mycallb ) return self . location
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[ "def", "_create_update_tracking_related_event", "(", "instance", ")", ":", "events", "=", "{", "}", "# Create a dict mapping related model field to modified fields", "for", "field", ",", "related_fields", "in", "instance", ".", "_tracked_related_fields", ".", "items", "(", ")", ":", "if", "not", "isinstance", "(", "instance", ".", "_meta", ".", "get_field", "(", "field", ")", ",", "ManyToManyField", ")", ":", "if", "isinstance", "(", "instance", ".", "_meta", ".", "get_field", "(", "field", ")", ",", "ForeignKey", ")", ":", "# Compare pk", "value", "=", "getattr", "(", "instance", ",", "'{0}_id'", ".", "format", "(", "field", ")", ")", "else", ":", "value", "=", "getattr", "(", "instance", ",", "field", ")", "if", "instance", ".", "_original_fields", "[", "field", "]", "!=", "value", ":", "for", "related_field", "in", "related_fields", ":", "events", ".", "setdefault", "(", "related_field", ",", "[", "]", ")", ".", "append", "(", "field", ")", "# Create the events from the events dict", "for", "related_field", ",", "fields", "in", "events", ".", "items", "(", ")", ":", "try", ":", "related_instances", "=", "getattr", "(", "instance", ",", "related_field", "[", "1", "]", ")", "except", "ObjectDoesNotExist", ":", "continue", "# FIXME: isinstance(related_instances, RelatedManager ?)", "if", "hasattr", "(", "related_instances", ",", "'all'", ")", ":", "related_instances", "=", "related_instances", ".", "all", "(", ")", "else", ":", "related_instances", "=", "[", "related_instances", "]", "for", "related_instance", "in", "related_instances", ":", "event", "=", "_create_event", "(", "related_instance", ",", "UPDATE", ")", "for", "field", "in", "fields", ":", "fieldname", "=", "'{0}__{1}'", ".", "format", "(", "related_field", "[", "0", "]", ",", "field", ")", "_create_tracked_field", "(", "event", ",", "instance", ",", "field", ",", "fieldname", "=", "fieldname", ")" ]
Convenience method to request the group from the device
def get_group ( self , callb = None ) : if self . group is None : mypartial = partial ( self . resp_set_group ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) response = self . req_with_resp ( GetGroup , StateGroup , callb = callb ) return self . group
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[ "def", "document_type", "(", "self", ",", "key", ",", "value", ")", ":", "schema", "=", "load_schema", "(", "'hep'", ")", "publication_type_schema", "=", "schema", "[", "'properties'", "]", "[", "'publication_type'", "]", "valid_publication_types", "=", "publication_type_schema", "[", "'items'", "]", "[", "'enum'", "]", "document_type", "=", "self", ".", "get", "(", "'document_type'", ",", "[", "]", ")", "publication_type", "=", "self", ".", "get", "(", "'publication_type'", ",", "[", "]", ")", "a_values", "=", "force_list", "(", "value", ".", "get", "(", "'a'", ")", ")", "for", "a_value", "in", "a_values", ":", "normalized_a_value", "=", "a_value", ".", "strip", "(", ")", ".", "lower", "(", ")", "if", "normalized_a_value", "==", "'arxiv'", ":", "continue", "# XXX: ignored.", "elif", "normalized_a_value", "==", "'citeable'", ":", "self", "[", "'citeable'", "]", "=", "True", "elif", "normalized_a_value", "==", "'core'", ":", "self", "[", "'core'", "]", "=", "True", "elif", "normalized_a_value", "==", "'noncore'", ":", "self", "[", "'core'", "]", "=", "False", "elif", "normalized_a_value", "==", "'published'", ":", "self", "[", "'refereed'", "]", "=", "True", "elif", "normalized_a_value", "==", "'withdrawn'", ":", "self", "[", "'withdrawn'", "]", "=", "True", "elif", "normalized_a_value", "==", "'deleted'", ":", "self", "[", "'deleted'", "]", "=", "True", "elif", "normalized_a_value", "in", "COLLECTIONS_MAP", ":", "self", ".", "setdefault", "(", "'_collections'", ",", "[", "]", ")", ".", "append", "(", "COLLECTIONS_MAP", "[", "normalized_a_value", "]", ")", "elif", "normalized_a_value", "in", "DOCUMENT_TYPE_MAP", ":", "document_type", ".", "append", "(", "DOCUMENT_TYPE_MAP", "[", "normalized_a_value", "]", ")", "elif", "normalized_a_value", "in", "valid_publication_types", ":", "publication_type", ".", "append", "(", "normalized_a_value", ")", "c_value", "=", "force_single_element", "(", "value", ".", "get", "(", "'c'", ",", "''", ")", ")", "normalized_c_value", "=", "c_value", ".", "strip", "(", ")", ".", "lower", "(", ")", "if", "normalized_c_value", "==", "'deleted'", ":", "self", "[", "'deleted'", "]", "=", "True", "self", "[", "'publication_type'", "]", "=", "publication_type", "return", "document_type" ]
Convenience method to request the wifi firmware info from the device
def get_wififirmware ( self , callb = None ) : if self . wifi_firmware_version is None : mypartial = partial ( self . resp_set_wififirmware ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) response = self . req_with_resp ( GetWifiFirmware , StateWifiFirmware , mycallb ) return ( self . wifi_firmware_version , self . wifi_firmware_build_timestamp )
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[ "def", "remove_targets", "(", "self", ",", "type", ",", "kept", "=", "None", ")", ":", "if", "kept", "is", "None", ":", "kept", "=", "[", "i", "for", "i", ",", "x", "in", "enumerate", "(", "self", ".", "_targets", ")", "if", "not", "isinstance", "(", "x", ",", "type", ")", "]", "if", "len", "(", "kept", ")", "==", "len", "(", "self", ".", "_targets", ")", ":", "return", "self", "self", ".", "_targets", "=", "[", "self", ".", "_targets", "[", "x", "]", "for", "x", "in", "kept", "]", "self", ".", "_labels", "=", "[", "self", ".", "_labels", "[", "x", "]", "for", "x", "in", "kept", "]", "if", "not", "self", ".", "_groups", ":", "return", "self", "index_map", "=", "{", "o_idx", ":", "n_idx", "for", "n_idx", ",", "o_idx", "in", "zip", "(", "range", "(", "len", "(", "self", ".", "_targets", ")", ")", ",", "kept", ")", "}", "kept", "=", "set", "(", "kept", ")", "for", "idx", ",", "grp", "in", "enumerate", "(", "self", ".", "_groups", ")", ":", "self", ".", "_groups", "[", "idx", "]", "=", "_sos_group", "(", "[", "index_map", "[", "x", "]", "for", "x", "in", "grp", ".", "_indexes", "if", "x", "in", "kept", "]", ",", "[", "y", "for", "x", ",", "y", "in", "zip", "(", "grp", ".", "_indexes", ",", "grp", ".", "_labels", ")", "if", "x", "in", "kept", "]", ")", ".", "set", "(", "*", "*", "grp", ".", "_dict", ")", "return", "self" ]
Default callback for get_wififirmware
def resp_set_wififirmware ( self , resp ) : if resp : self . wifi_firmware_version = float ( str ( str ( resp . version >> 16 ) + "." + str ( resp . version & 0xff ) ) ) self . wifi_firmware_build_timestamp = resp . build
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[ "def", "touch_object", "(", "self", ",", "objects", ":", "Set", "[", "Object", "]", ")", "->", "Set", "[", "Object", "]", ":", "objects_per_box", "=", "self", ".", "_separate_objects_by_boxes", "(", "objects", ")", "return_set", "=", "set", "(", ")", "for", "box", ",", "box_objects", "in", "objects_per_box", ".", "items", "(", ")", ":", "candidate_objects", "=", "box", ".", "objects", "for", "object_", "in", "box_objects", ":", "for", "candidate_object", "in", "candidate_objects", ":", "if", "self", ".", "_objects_touch_each_other", "(", "object_", ",", "candidate_object", ")", ":", "return_set", ".", "add", "(", "candidate_object", ")", "return", "return_set" ]
Convenience method to request the wifi info from the device
def get_wifiinfo ( self , callb = None ) : response = self . req_with_resp ( GetWifiInfo , StateWifiInfo , callb = callb ) return None
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[ "def", "_modify_report", "(", "summary_path", ",", "out_dir", ")", ":", "summary_path", "=", "op", ".", "abspath", "(", "summary_path", ")", "template", "=", "op", ".", "normpath", "(", "op", ".", "join", "(", "op", ".", "dirname", "(", "op", ".", "realpath", "(", "template_seqcluster", ".", "__file__", ")", ")", ",", "\"report.rmd\"", ")", ")", "content", "=", "open", "(", "template", ")", ".", "read", "(", ")", "out_content", "=", "string", ".", "Template", "(", "content", ")", ".", "safe_substitute", "(", "{", "'path_abs'", ":", "summary_path", "}", ")", "out_file", "=", "op", ".", "join", "(", "out_dir", ",", "\"srna_report.rmd\"", ")", "with", "open", "(", "out_file", ",", "'w'", ")", "as", "out_handle", ":", "out_handle", ".", "write", "(", "out_content", ")", "return", "out_file" ]
Convenience method to request the device firmware info from the device
def get_hostfirmware ( self , callb = None ) : if self . host_firmware_version is None : mypartial = partial ( self . resp_set_hostfirmware ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) response = self . req_with_resp ( GetHostFirmware , StateHostFirmware , mycallb ) return ( self . host_firmware_version , self . host_firmware_build_timestamp )
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[ "def", "option", "(", "self", ",", "key", ",", "value", "=", "None", ",", "*", "*", "kwargs", ")", ":", "if", "not", "isinstance", "(", "self", ".", "_container", ",", "Section", ")", ":", "raise", "ValueError", "(", "\"Options can only be added inside a section!\"", ")", "option", "=", "Option", "(", "key", ",", "value", ",", "container", "=", "self", ".", "_container", ",", "*", "*", "kwargs", ")", "option", ".", "value", "=", "value", "self", ".", "_container", ".", "structure", ".", "insert", "(", "self", ".", "_idx", ",", "option", ")", "self", ".", "_idx", "+=", "1", "return", "self" ]
Default callback for get_hostfirmware
def resp_set_hostfirmware ( self , resp ) : if resp : self . host_firmware_version = float ( str ( str ( resp . version >> 16 ) + "." + str ( resp . version & 0xff ) ) ) self . host_firmware_build_timestamp = resp . build
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[ "def", "_set_local_file_path", "(", "self", ")", ":", "self", ".", "FILE_LOCAL", "=", "self", ".", "_transfer", ".", "get_env", "(", "'FILE_LOCAL'", ")", "if", "not", "self", ".", "FILE_LOCAL", ":", "filename", "=", "'{}_{}.{}'", ".", "format", "(", "str", "(", "self", ".", "_transfer", ".", "prefix", ")", ",", "str", "(", "self", ".", "_transfer", ".", "namespace", ")", ",", "str", "(", "self", ".", "file_extension", ")", ")", "self", ".", "FILE_LOCAL", "=", "os", ".", "path", ".", "join", "(", "os", ".", "path", ".", "expanduser", "(", "\"~\"", ")", ",", "filename", ")", "dirs", "=", "os", ".", "path", ".", "dirname", "(", "self", ".", "FILE_LOCAL", ")", "if", "not", "os", ".", "path", ".", "exists", "(", "dirs", ")", ":", "os", ".", "makedirs", "(", "dirs", ")", "try", ":", "open", "(", "self", ".", "FILE_LOCAL", ",", "\"rb+\"", ")", ".", "close", "(", ")", "except", ":", "open", "(", "self", ".", "FILE_LOCAL", ",", "\"a\"", ")", ".", "close", "(", ")" ]
Convenience method to request the device info from the device
def get_hostinfo ( self , callb = None ) : response = self . req_with_resp ( GetInfo , StateInfo , callb = callb ) return None
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[ "def", "option", "(", "self", ",", "key", ",", "value", "=", "None", ",", "*", "*", "kwargs", ")", ":", "if", "not", "isinstance", "(", "self", ".", "_container", ",", "Section", ")", ":", "raise", "ValueError", "(", "\"Options can only be added inside a section!\"", ")", "option", "=", "Option", "(", "key", ",", "value", ",", "container", "=", "self", ".", "_container", ",", "*", "*", "kwargs", ")", "option", ".", "value", "=", "value", "self", ".", "_container", ".", "structure", ".", "insert", "(", "self", ".", "_idx", ",", "option", ")", "self", ".", "_idx", "+=", "1", "return", "self" ]
Convenience method to request the version from the device
def get_version ( self , callb = None ) : if self . vendor is None : mypartial = partial ( self . resp_set_version ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) response = self . req_with_resp ( GetVersion , StateVersion , callb = mycallb ) return ( self . host_firmware_version , self . host_firmware_build_timestamp )
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[ "def", "setOverlayTextureColorSpace", "(", "self", ",", "ulOverlayHandle", ",", "eTextureColorSpace", ")", ":", "fn", "=", "self", ".", "function_table", ".", "setOverlayTextureColorSpace", "result", "=", "fn", "(", "ulOverlayHandle", ",", "eTextureColorSpace", ")", "return", "result" ]
Default callback for get_version
def resp_set_version ( self , resp ) : if resp : self . vendor = resp . vendor self . product = resp . product self . version = resp . version
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[ "def", "read_frames", "(", "cls", ",", "reader", ")", ":", "rval", "=", "deque", "(", ")", "while", "True", ":", "frame_start_pos", "=", "reader", ".", "tell", "(", ")", "try", ":", "frame", "=", "Frame", ".", "_read_frame", "(", "reader", ")", "except", "Reader", ".", "BufferUnderflow", ":", "# No more data in the stream", "frame", "=", "None", "except", "Reader", ".", "ReaderError", "as", "e", ":", "# Some other format error", "raise", "Frame", ".", "FormatError", ",", "str", "(", "e", ")", ",", "sys", ".", "exc_info", "(", ")", "[", "-", "1", "]", "except", "struct", ".", "error", "as", "e", ":", "raise", "Frame", ".", "FormatError", ",", "str", "(", "e", ")", ",", "sys", ".", "exc_info", "(", ")", "[", "-", "1", "]", "if", "frame", "is", "None", ":", "reader", ".", "seek", "(", "frame_start_pos", ")", "break", "rval", ".", "append", "(", "frame", ")", "return", "rval" ]
Default callback for set_power
def resp_set_lightpower ( self , resp , power_level = None ) : if power_level is not None : self . power_level = power_level elif resp : self . power_level = resp . power_level
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[ "def", "construct_error_message", "(", "driver_id", ",", "error_type", ",", "message", ",", "timestamp", ")", ":", "builder", "=", "flatbuffers", ".", "Builder", "(", "0", ")", "driver_offset", "=", "builder", ".", "CreateString", "(", "driver_id", ".", "binary", "(", ")", ")", "error_type_offset", "=", "builder", ".", "CreateString", "(", "error_type", ")", "message_offset", "=", "builder", ".", "CreateString", "(", "message", ")", "ray", ".", "core", ".", "generated", ".", "ErrorTableData", ".", "ErrorTableDataStart", "(", "builder", ")", "ray", ".", "core", ".", "generated", ".", "ErrorTableData", ".", "ErrorTableDataAddDriverId", "(", "builder", ",", "driver_offset", ")", "ray", ".", "core", ".", "generated", ".", "ErrorTableData", ".", "ErrorTableDataAddType", "(", "builder", ",", "error_type_offset", ")", "ray", ".", "core", ".", "generated", ".", "ErrorTableData", ".", "ErrorTableDataAddErrorMessage", "(", "builder", ",", "message_offset", ")", "ray", ".", "core", ".", "generated", ".", "ErrorTableData", ".", "ErrorTableDataAddTimestamp", "(", "builder", ",", "timestamp", ")", "error_data_offset", "=", "ray", ".", "core", ".", "generated", ".", "ErrorTableData", ".", "ErrorTableDataEnd", "(", "builder", ")", "builder", ".", "Finish", "(", "error_data_offset", ")", "return", "bytes", "(", "builder", ".", "Output", "(", ")", ")" ]
Convenience method to request the colour status from the device
def get_color ( self , callb = None ) : response = self . req_with_resp ( LightGet , LightState , callb = callb ) return self . color
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[ "def", "get_partition", "(", "self", ",", "num_x", "=", "1", ",", "num_y", "=", "1", ")", ":", "size_x", ",", "size_y", "=", "(", "self", ".", "max_x", "-", "self", ".", "min_x", ")", "/", "num_x", ",", "(", "self", ".", "max_y", "-", "self", ".", "min_y", ")", "/", "num_y", "return", "[", "[", "BBox", "(", "[", "self", ".", "min_x", "+", "i", "*", "size_x", ",", "self", ".", "min_y", "+", "j", "*", "size_y", ",", "self", ".", "min_x", "+", "(", "i", "+", "1", ")", "*", "size_x", ",", "self", ".", "min_y", "+", "(", "j", "+", "1", ")", "*", "size_y", "]", ",", "crs", "=", "self", ".", "crs", ")", "for", "j", "in", "range", "(", "num_y", ")", "]", "for", "i", "in", "range", "(", "num_x", ")", "]" ]
Convenience method to set the colour status of the device
def set_color ( self , value , callb = None , duration = 0 , rapid = False ) : if len ( value ) == 4 : mypartial = partial ( self . resp_set_light , color = value ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) #try: if rapid : self . fire_and_forget ( LightSetColor , { "color" : value , "duration" : duration } , num_repeats = 1 ) self . resp_set_light ( None , color = value ) if callb : callb ( self , None ) else : self . req_with_ack ( LightSetColor , { "color" : value , "duration" : duration } , callb = mycallb )
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[ "def", "_GetFileMappingsByPath", "(", "self", ",", "key_path_upper", ")", ":", "candidate_mappings", "=", "[", "]", "for", "mapping", "in", "self", ".", "_REGISTRY_FILE_MAPPINGS_NT", ":", "if", "key_path_upper", ".", "startswith", "(", "mapping", ".", "key_path_prefix", ".", "upper", "(", ")", ")", ":", "candidate_mappings", ".", "append", "(", "mapping", ")", "# Sort the candidate mappings by longest (most specific) match first.", "candidate_mappings", ".", "sort", "(", "key", "=", "lambda", "mapping", ":", "len", "(", "mapping", ".", "key_path_prefix", ")", ",", "reverse", "=", "True", ")", "for", "mapping", "in", "candidate_mappings", ":", "yield", "mapping" ]
Default callback for set_color
def resp_set_light ( self , resp , color = None ) : if color : self . color = color elif resp : self . power_level = resp . power_level self . color = resp . color self . label = resp . label . decode ( ) . replace ( "\x00" , "" )
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Convenience method to request the state of colour by zones from the device
def get_color_zones ( self , start_index , end_index = None , callb = None ) : if end_index is None : end_index = start_index + 7 args = { "start_index" : start_index , "end_index" : end_index , } self . req_with_resp ( MultiZoneGetColorZones , MultiZoneStateMultiZone , payload = args , callb = callb )
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https://github.com/frawau/aiolifx/blob/9bd8c5e6d291f4c79314989402f7e2c6476d5851/aiolifx/aiolifx.py#L908-L930
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Convenience method to set the colour status zone of the device
def set_color_zones ( self , start_index , end_index , color , duration = 0 , apply = 1 , callb = None , rapid = False ) : if len ( color ) == 4 : args = { "start_index" : start_index , "end_index" : end_index , "color" : color , "duration" : duration , "apply" : apply , } mypartial = partial ( self . resp_set_multizonemultizone , args = args ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) if rapid : self . fire_and_forget ( MultiZoneSetColorZones , args , num_repeats = 1 ) mycallb ( self , None ) else : self . req_with_ack ( MultiZoneSetColorZones , args , callb = mycallb )
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Convenience method to request the infrared brightness from the device
def get_infrared ( self , callb = None ) : response = self . req_with_resp ( LightGetInfrared , LightStateInfrared , callb = callb ) return self . infrared_brightness
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https://github.com/frawau/aiolifx/blob/9bd8c5e6d291f4c79314989402f7e2c6476d5851/aiolifx/aiolifx.py#L1045-L1060
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Convenience method to set the infrared status of the device
def set_infrared ( self , infrared_brightness , callb = None , rapid = False ) : mypartial = partial ( self . resp_set_infrared , infrared_brightness = infrared_brightness ) if callb : mycallb = lambda x , y : ( mypartial ( y ) , callb ( x , y ) ) else : mycallb = lambda x , y : mypartial ( y ) if rapid : self . fire_and_forget ( LightSetInfrared , { "infrared_brightness" : infrared_brightness } , num_repeats = 1 ) self . resp_set_infrared ( None , infrared_brightness = infrared_brightness ) if callb : callb ( self , None ) else : self . req_with_ack ( LightSetInfrared , { "infrared_brightness" : infrared_brightness } , callb = mycallb )
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Start discovery task .
def start ( self , listen_ip = LISTEN_IP , listen_port = 0 ) : coro = self . loop . create_datagram_endpoint ( lambda : self , local_addr = ( listen_ip , listen_port ) ) self . task = self . loop . create_task ( coro ) return self . task
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https://github.com/frawau/aiolifx/blob/9bd8c5e6d291f4c79314989402f7e2c6476d5851/aiolifx/aiolifx.py#L1150-L1156
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Method run when the UDP broadcast server is started
def connection_made ( self , transport ) : #print('started') self . transport = transport sock = self . transport . get_extra_info ( "socket" ) sock . setsockopt ( socket . SOL_SOCKET , socket . SO_REUSEADDR , 1 ) sock . setsockopt ( socket . SOL_SOCKET , socket . SO_BROADCAST , 1 ) self . loop . call_soon ( self . discover )
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https://github.com/frawau/aiolifx/blob/9bd8c5e6d291f4c79314989402f7e2c6476d5851/aiolifx/aiolifx.py#L1158-L1166
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Method run when data is received from the devices
def datagram_received ( self , data , addr ) : response = unpack_lifx_message ( data ) response . ip_addr = addr [ 0 ] mac_addr = response . target_addr if mac_addr == BROADCAST_MAC : return if type ( response ) == StateService and response . service == 1 : # only look for UDP services # discovered remote_port = response . port elif type ( response ) == LightState : # looks like the lights are volunteering LigthState after booting remote_port = UDP_BROADCAST_PORT else : return if self . ipv6prefix : family = socket . AF_INET6 remote_ip = mac_to_ipv6_linklocal ( mac_addr , self . ipv6prefix ) else : family = socket . AF_INET remote_ip = response . ip_addr if mac_addr in self . lights : # rediscovered light = self . lights [ mac_addr ] # nothing to do if light . registered : return light . cleanup ( ) light . ip_addr = remote_ip light . port = remote_port else : # newly discovered light = Light ( self . loop , mac_addr , remote_ip , remote_port , parent = self ) self . lights [ mac_addr ] = light coro = self . loop . create_datagram_endpoint ( lambda : light , family = family , remote_addr = ( remote_ip , remote_port ) ) light . task = self . loop . create_task ( coro )
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Method to send a discovery message
def discover ( self ) : if self . transport : if self . discovery_countdown <= 0 : self . discovery_countdown = self . discovery_interval msg = GetService ( BROADCAST_MAC , self . source_id , seq_num = 0 , payload = { } , ack_requested = False , response_requested = True ) self . transport . sendto ( msg . generate_packed_message ( ) , ( self . broadcast_ip , UDP_BROADCAST_PORT ) ) else : self . discovery_countdown -= self . discovery_step self . loop . call_later ( self . discovery_step , self . discover )
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https://github.com/frawau/aiolifx/blob/9bd8c5e6d291f4c79314989402f7e2c6476d5851/aiolifx/aiolifx.py#L1224-L1234
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Return a list of local IP addresses on interfaces with LIFX bulbs .
async def scan ( self , timeout = 1 ) : adapters = await self . loop . run_in_executor ( None , ifaddr . get_adapters ) ips = [ ip . ip for adapter in ifaddr . get_adapters ( ) for ip in adapter . ips if ip . is_IPv4 ] if not ips : return [ ] tasks = [ ] discoveries = [ ] for ip in ips : manager = ScanManager ( ip ) lifx_discovery = LifxDiscovery ( self . loop , manager ) discoveries . append ( lifx_discovery ) lifx_discovery . start ( listen_ip = ip ) tasks . append ( self . loop . create_task ( manager . lifx_ip ( ) ) ) ( done , pending ) = await aio . wait ( tasks , timeout = timeout ) for discovery in discoveries : discovery . cleanup ( ) for task in pending : task . cancel ( ) return [ task . result ( ) for task in done ]
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High level import function that tries to determine the specific version of the data format used .
def _get_file_version ( filename ) : mat = sio . loadmat ( filename , squeeze_me = True ) version = mat [ 'MP' ] [ 'Version' ] . item ( ) del ( mat ) return version
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https://github.com/geophysics-ubonn/reda/blob/46a939729e40c7c4723315c03679c40761152e9e/lib/reda/importers/eit_fzj.py#L34-L54
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Given a MD DataFrame return a Nx4 array which permutes the current injection dipoles .
def MD_ConfigsPermutate ( df_md ) : g_current_injections = df_md . groupby ( [ 'a' , 'b' ] ) ab = np . array ( list ( g_current_injections . groups . keys ( ) ) ) config_mgr = ConfigManager ( nr_of_electrodes = ab . max ( ) ) config_mgr . gen_configs_permutate ( ab , silent = True ) return config_mgr . configs
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https://github.com/geophysics-ubonn/reda/blob/46a939729e40c7c4723315c03679c40761152e9e/lib/reda/importers/eit_fzj.py#L57-L65
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Apply correction factors for a pseudo - 2D measurement setup . See Weigand and Kemna 2017 Biogeosciences for detailed information .
def apply_correction_factors ( df , correction_file ) : if isinstance ( correction_file , ( list , tuple ) ) : corr_data_raw = np . vstack ( [ np . loadtxt ( x ) for x in correction_file ] ) else : corr_data_raw = np . loadtxt ( correction_file ) if corr_data_raw . shape [ 1 ] == 3 : A = ( corr_data_raw [ : , 0 ] / 1e4 ) . astype ( int ) B = ( corr_data_raw [ : , 0 ] % 1e4 ) . astype ( int ) M = ( corr_data_raw [ : , 1 ] / 1e4 ) . astype ( int ) N = ( corr_data_raw [ : , 1 ] % 1e4 ) . astype ( int ) corr_data = np . vstack ( ( A , B , M , N , corr_data_raw [ : , 2 ] ) ) . T elif corr_data_raw . shape [ 1 ] == 5 : corr_data = corr_data_raw else : raise Exception ( 'error' ) corr_data [ : , 0 : 2 ] = np . sort ( corr_data [ : , 0 : 2 ] , axis = 1 ) corr_data [ : , 2 : 4 ] = np . sort ( corr_data [ : , 2 : 4 ] , axis = 1 ) if 'frequency' not in df . columns : raise Exception ( 'No frequency data found. Are you sure this is a seit data set?' ) df = df . reset_index ( ) gf = df . groupby ( [ 'a' , 'b' , 'm' , 'n' ] ) for key , item in gf . indices . items ( ) : # print('key', key) # print(item) item_norm = np . hstack ( ( np . sort ( key [ 0 : 2 ] ) , np . sort ( key [ 2 : 4 ] ) ) ) # print(item_norm) index = np . where ( ( corr_data [ : , 0 ] == item_norm [ 0 ] ) & ( corr_data [ : , 1 ] == item_norm [ 1 ] ) & ( corr_data [ : , 2 ] == item_norm [ 2 ] ) & ( corr_data [ : , 3 ] == item_norm [ 3 ] ) ) [ 0 ] # print(index, corr_data[index]) if len ( index ) == 0 : print ( key ) import IPython IPython . embed ( ) raise Exception ( 'No correction factor found for this configuration' ) factor = corr_data [ index , 4 ] # if key == (1, 4, 2, 3): # print(key) # print(factor) # print(df['R']) # print(df['k']) # import IPython # IPython.embed() # exit() # apply correction factor for col in ( 'r' , 'Zt' , 'Vmn' , 'rho_a' ) : if col in df . columns : df . ix [ item , col ] *= factor df . ix [ item , 'corr_fac' ] = factor return df , corr_data
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https://github.com/geophysics-ubonn/reda/blob/46a939729e40c7c4723315c03679c40761152e9e/lib/reda/importers/eit_fzj.py#L217-L283
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Returns a function for calculation of probability matrix of substitutions i - > j over time t .
def get_pij_method ( model = F81 , frequencies = None , kappa = None ) : if is_f81_like ( model ) : mu = get_mu ( frequencies ) return lambda t : get_f81_pij ( t , frequencies , mu ) if JTT == model : return get_jtt_pij if HKY == model : return lambda t : get_hky_pij ( t , frequencies , kappa )
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https://github.com/evolbioinfo/pastml/blob/df8a375841525738383e59548eed3441b07dbd3e/pastml/ml.py#L87-L106
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Initializes the allowed state arrays for tips based on their states given by the feature .
def initialize_allowed_states ( tree , feature , states ) : allowed_states_feature = get_personalized_feature_name ( feature , ALLOWED_STATES ) state2index = dict ( zip ( states , range ( len ( states ) ) ) ) for node in tree . traverse ( ) : node_states = getattr ( node , feature , set ( ) ) if not node_states : allowed_states = np . ones ( len ( state2index ) , dtype = np . int ) else : allowed_states = np . zeros ( len ( state2index ) , dtype = np . int ) for state in node_states : allowed_states [ state2index [ state ] ] = 1 node . add_feature ( allowed_states_feature , allowed_states )
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https://github.com/evolbioinfo/pastml/blob/df8a375841525738383e59548eed3441b07dbd3e/pastml/ml.py#L309-L333
[ "def", "cancelOrder", "(", "self", ",", "orderId", ")", ":", "self", ".", "ibConn", ".", "cancelOrder", "(", "orderId", ")", "# update order id for next time", "self", ".", "requestOrderIds", "(", ")", "return", "orderId" ]
Alters the bottom - up likelihood arrays for zero - distance tips to make sure they do not contradict with other zero - distance tip siblings .
def alter_zero_tip_allowed_states ( tree , feature ) : zero_parent2tips = defaultdict ( list ) allowed_state_feature = get_personalized_feature_name ( feature , ALLOWED_STATES ) for tip in tree : if tip . dist == 0 : state = getattr ( tip , feature , None ) if state is not None and state != '' : zero_parent2tips [ tip . up ] . append ( tip ) # adjust zero tips to contain all the zero tip options as states for parent , zero_tips in zero_parent2tips . items ( ) : # If there is a common state do nothing counts = None for tip in zero_tips : if counts is None : counts = getattr ( tip , allowed_state_feature ) . copy ( ) else : counts += getattr ( tip , allowed_state_feature ) if counts . max ( ) == len ( zero_tips ) : continue # Otherwise set all tip states to state union allowed_states = None for tip in zero_tips : if allowed_states is None : allowed_states = getattr ( tip , allowed_state_feature ) . copy ( ) else : tip_allowed_states = getattr ( tip , allowed_state_feature ) allowed_states [ np . nonzero ( tip_allowed_states ) ] = 1 tip . add_feature ( allowed_state_feature , allowed_states )
8,467
https://github.com/evolbioinfo/pastml/blob/df8a375841525738383e59548eed3441b07dbd3e/pastml/ml.py#L336-L375
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Unalters the bottom - up likelihood arrays for zero - distance tips to contain ones only in their states .
def unalter_zero_tip_allowed_states ( tree , feature , state2index ) : allowed_state_feature = get_personalized_feature_name ( feature , ALLOWED_STATES ) for tip in tree : if tip . dist > 0 : continue state = getattr ( tip , feature , set ( ) ) if state : initial_allowed_states = np . zeros ( len ( state2index ) , np . int ) for _ in state : initial_allowed_states [ state2index [ _ ] ] = 1 allowed_states = getattr ( tip , allowed_state_feature ) & initial_allowed_states tip . add_feature ( allowed_state_feature , ( allowed_states if np . any ( allowed_states > 0 ) else initial_allowed_states ) )
8,468
https://github.com/evolbioinfo/pastml/blob/df8a375841525738383e59548eed3441b07dbd3e/pastml/ml.py#L378-L399
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Unalters the joint tip states for zero - distance tips to contain only their states .
def unalter_zero_tip_joint_states ( tree , feature , state2index ) : lh_joint_state_feature = get_personalized_feature_name ( feature , BU_LH_JOINT_STATES ) for tip in tree : if tip . dist > 0 : continue state = getattr ( tip , feature , set ( ) ) if len ( state ) > 1 : allowed_indices = { state2index [ _ ] for _ in state } allowed_index = next ( iter ( allowed_indices ) ) joint_states = getattr ( tip , lh_joint_state_feature ) for i in range ( len ( state2index ) ) : if joint_states [ i ] not in allowed_indices : joint_states [ i ] = allowed_index elif len ( state ) == 1 : tip . add_feature ( lh_joint_state_feature , np . ones ( len ( state2index ) , np . int ) * state2index [ next ( iter ( state ) ) ] )
8,469
https://github.com/evolbioinfo/pastml/blob/df8a375841525738383e59548eed3441b07dbd3e/pastml/ml.py#L402-L425
[ "def", "Load", "(", "self", ")", ":", "for", "record", "in", "super", "(", "EventFileLoader", ",", "self", ")", ".", "Load", "(", ")", ":", "yield", "event_pb2", ".", "Event", ".", "FromString", "(", "record", ")" ]
Calculates marginal likelihoods for each tree node by multiplying state frequencies with their bottom - up and top - down likelihoods .
def calculate_marginal_likelihoods ( tree , feature , frequencies ) : bu_lh_feature = get_personalized_feature_name ( feature , BU_LH ) bu_lh_sf_feature = get_personalized_feature_name ( feature , BU_LH_SF ) td_lh_feature = get_personalized_feature_name ( feature , TD_LH ) td_lh_sf_feature = get_personalized_feature_name ( feature , TD_LH_SF ) lh_feature = get_personalized_feature_name ( feature , LH ) lh_sf_feature = get_personalized_feature_name ( feature , LH_SF ) allowed_state_feature = get_personalized_feature_name ( feature , ALLOWED_STATES ) for node in tree . traverse ( 'preorder' ) : likelihood = getattr ( node , bu_lh_feature ) * getattr ( node , td_lh_feature ) * frequencies * getattr ( node , allowed_state_feature ) node . add_feature ( lh_feature , likelihood ) node . add_feature ( lh_sf_feature , getattr ( node , td_lh_sf_feature ) + getattr ( node , bu_lh_sf_feature ) ) node . del_feature ( bu_lh_feature ) node . del_feature ( bu_lh_sf_feature ) node . del_feature ( td_lh_feature ) node . del_feature ( td_lh_sf_feature )
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https://github.com/evolbioinfo/pastml/blob/df8a375841525738383e59548eed3441b07dbd3e/pastml/ml.py#L428-L455
[ "def", "hide_tool", "(", "self", ",", "context_name", ",", "tool_name", ")", ":", "data", "=", "self", ".", "_context", "(", "context_name", ")", "hidden_tools", "=", "data", "[", "\"hidden_tools\"", "]", "if", "tool_name", "not", "in", "hidden_tools", ":", "self", ".", "_validate_tool", "(", "context_name", ",", "tool_name", ")", "hidden_tools", ".", "add", "(", "tool_name", ")", "self", ".", "_flush_tools", "(", ")" ]
Normalizes each node marginal likelihoods to convert them to marginal probabilities .
def convert_likelihoods_to_probabilities ( tree , feature , states ) : lh_feature = get_personalized_feature_name ( feature , LH ) name2probs = { } for node in tree . traverse ( ) : lh = getattr ( node , lh_feature ) name2probs [ node . name ] = lh / lh . sum ( ) return pd . DataFrame . from_dict ( name2probs , orient = 'index' , columns = states )
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https://github.com/evolbioinfo/pastml/blob/df8a375841525738383e59548eed3441b07dbd3e/pastml/ml.py#L476-L493
[ "def", "_overlapping", "(", "files", ")", ":", "segments", "=", "set", "(", ")", "for", "path", "in", "files", ":", "seg", "=", "file_segment", "(", "path", ")", "for", "s", "in", "segments", ":", "if", "seg", ".", "intersects", "(", "s", ")", ":", "return", "True", "segments", ".", "add", "(", "seg", ")", "return", "False" ]
Chooses node ancestral states based on their marginal probabilities using MPPA method .
def choose_ancestral_states_mppa ( tree , feature , states , force_joint = True ) : lh_feature = get_personalized_feature_name ( feature , LH ) allowed_state_feature = get_personalized_feature_name ( feature , ALLOWED_STATES ) joint_state_feature = get_personalized_feature_name ( feature , JOINT_STATE ) n = len ( states ) _ , state2array = get_state2allowed_states ( states , False ) num_scenarios = 1 unresolved_nodes = 0 num_states = 0 # If force_joint == True, # we make sure that the joint state is always chosen, # for this we sort the marginal probabilities array as [lowest_non_joint_mp, ..., highest_non_joint_mp, joint_mp] # select k in 1:n such as the correction between choosing 0, 0, ..., 1/k, ..., 1/k and our sorted array is min # and return the corresponding states for node in tree . traverse ( ) : marginal_likelihoods = getattr ( node , lh_feature ) marginal_probs = marginal_likelihoods / marginal_likelihoods . sum ( ) if force_joint : joint_index = getattr ( node , joint_state_feature ) joint_prob = marginal_probs [ joint_index ] marginal_probs = np . hstack ( ( np . sort ( np . delete ( marginal_probs , joint_index ) ) , [ joint_prob ] ) ) else : marginal_probs = np . sort ( marginal_probs ) best_k = n best_correstion = np . inf for k in range ( 1 , n + 1 ) : correction = np . hstack ( ( np . zeros ( n - k ) , np . ones ( k ) / k ) ) - marginal_probs correction = correction . dot ( correction ) if correction < best_correstion : best_correstion = correction best_k = k num_scenarios *= best_k num_states += best_k if force_joint : indices_selected = sorted ( range ( n ) , key = lambda _ : ( 0 if n == joint_index else 1 , - marginal_likelihoods [ _ ] ) ) [ : best_k ] else : indices_selected = sorted ( range ( n ) , key = lambda _ : - marginal_likelihoods [ _ ] ) [ : best_k ] if best_k == 1 : allowed_states = state2array [ indices_selected [ 0 ] ] else : allowed_states = np . zeros ( len ( states ) , dtype = np . int ) allowed_states [ indices_selected ] = 1 unresolved_nodes += 1 node . add_feature ( allowed_state_feature , allowed_states ) return num_scenarios , unresolved_nodes , num_states
8,472
https://github.com/evolbioinfo/pastml/blob/df8a375841525738383e59548eed3441b07dbd3e/pastml/ml.py#L496-L563
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Chooses node ancestral states based on their marginal probabilities using MAP method .
def choose_ancestral_states_map ( tree , feature , states ) : lh_feature = get_personalized_feature_name ( feature , LH ) allowed_state_feature = get_personalized_feature_name ( feature , ALLOWED_STATES ) _ , state2array = get_state2allowed_states ( states , False ) for node in tree . traverse ( ) : marginal_likelihoods = getattr ( node , lh_feature ) node . add_feature ( allowed_state_feature , state2array [ marginal_likelihoods . argmax ( ) ] )
8,473
https://github.com/evolbioinfo/pastml/blob/df8a375841525738383e59548eed3441b07dbd3e/pastml/ml.py#L566-L582
[ "def", "console_wait_for_keypress", "(", "flush", ":", "bool", ")", "->", "Key", ":", "key", "=", "Key", "(", ")", "lib", ".", "TCOD_console_wait_for_keypress_wrapper", "(", "key", ".", "key_p", ",", "flush", ")", "return", "key" ]
Chooses node ancestral states based on their marginal probabilities using joint method .
def choose_ancestral_states_joint ( tree , feature , states , frequencies ) : lh_feature = get_personalized_feature_name ( feature , BU_LH ) lh_state_feature = get_personalized_feature_name ( feature , BU_LH_JOINT_STATES ) allowed_state_feature = get_personalized_feature_name ( feature , ALLOWED_STATES ) joint_state_feature = get_personalized_feature_name ( feature , JOINT_STATE ) _ , state2array = get_state2allowed_states ( states , False ) def chose_consistent_state ( node , state_index ) : node . add_feature ( joint_state_feature , state_index ) node . add_feature ( allowed_state_feature , state2array [ state_index ] ) for child in node . children : chose_consistent_state ( child , getattr ( child , lh_state_feature ) [ state_index ] ) chose_consistent_state ( tree , ( getattr ( tree , lh_feature ) * frequencies ) . argmax ( ) )
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https://github.com/evolbioinfo/pastml/blob/df8a375841525738383e59548eed3441b07dbd3e/pastml/ml.py#L585-L609
[ "def", "win32_refresh_window", "(", "cls", ")", ":", "# Get console handle", "handle", "=", "windll", ".", "kernel32", ".", "GetConsoleWindow", "(", ")", "RDW_INVALIDATE", "=", "0x0001", "windll", ".", "user32", ".", "RedrawWindow", "(", "handle", ",", "None", ",", "None", ",", "c_uint", "(", "RDW_INVALIDATE", ")", ")" ]
Reformats the column string to make sure it contains only numerical letter characters or underscore .
def col_name2cat ( column ) : column_string = '' . join ( s for s in column . replace ( ' ' , '_' ) if s . isalnum ( ) or '_' == s ) return column_string
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https://github.com/evolbioinfo/pastml/blob/df8a375841525738383e59548eed3441b07dbd3e/pastml/__init__.py#L14-L24
[ "def", "_parse_document", "(", "document", ":", "Path", ",", "system", ":", "System", "=", "None", ",", "profile", "=", "EProfile", ".", "FULL", ")", ":", "logger", ".", "debug", "(", "'parse document: {0}'", ".", "format", "(", "document", ")", ")", "stream", "=", "FileStream", "(", "str", "(", "document", ")", ",", "encoding", "=", "'utf-8'", ")", "system", "=", "FileSystem", ".", "_parse_stream", "(", "stream", ",", "system", ",", "document", ",", "profile", ")", "FileSystem", ".", "merge_annotations", "(", "system", ",", "document", ".", "stripext", "(", ")", "+", "'.yaml'", ")", "return", "system" ]
Get user config filename .
def get_user_config_filename ( appname = 'notify' ) : import platform system = platform . system ( ) if system == 'Windows' : rootname = os . path . join ( os . environ [ 'APPDATA' ] , appname ) filename = appname + ".cfg" prefix = '' elif system == 'Linux' : XDG_CONFIG_HOME = os . environ . get ( 'XDG_CONFIG_HOME' , None ) rootname = XDG_CONFIG_HOME or os . path . join ( '~' , '.config' ) rootname = os . path . expanduser ( rootname ) # check if XDG_CONFIG_HOME exists if not os . path . exists ( rootname ) and XDG_CONFIG_HOME is None : # XDG_CONFIG_HOME is not used rootname = os . path . expanduser ( '~' ) filename = appname + ".cfg" prefix = '.' else : rootname = os . path . join ( rootname , appname ) filename = appname + ".cfg" prefix = '' elif system == 'Darwin' : rootname = os . path . expanduser ( '~' ) filename = appname + ".cfg" prefix = '.' else : # Unknown rootname = os . path . expanduser ( '~' ) filename = appname + ".cfg" prefix = '' return os . path . join ( rootname , prefix + filename )
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https://github.com/lambdalisue/notify/blob/1b6d7d1faa2cea13bfaa1f35130f279a0115e686/src/notify/conf.py#L24-L70
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Convert ConfigParser instance to argparse . Namespace
def config_to_options ( config ) : class Options : host = config . get ( 'smtp' , 'host' , raw = True ) port = config . getint ( 'smtp' , 'port' ) to_addr = config . get ( 'mail' , 'to_addr' , raw = True ) from_addr = config . get ( 'mail' , 'from_addr' , raw = True ) subject = config . get ( 'mail' , 'subject' , raw = True ) encoding = config . get ( 'mail' , 'encoding' , raw = True ) username = config . get ( 'auth' , 'username' ) opts = Options ( ) # format opts . from_addr % { 'host' : opts . host , 'prog' : 'notify' } opts . to_addr % { 'host' : opts . host , 'prog' : 'notify' } return opts
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https://github.com/lambdalisue/notify/blob/1b6d7d1faa2cea13bfaa1f35130f279a0115e686/src/notify/conf.py#L73-L99
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Create default ConfigParser instance
def create_default_config ( ) : import codecs config = ConfigParser . SafeConfigParser ( ) config . readfp ( StringIO ( DEFAULT_CONFIG ) ) # Load user settings filename = get_user_config_filename ( ) if not os . path . exists ( filename ) : from wizard import setup_wizard setup_wizard ( config ) else : try : fi = codecs . open ( filename , 'r' , encoding = 'utf-8' ) config . readfp ( fi ) finally : fi . close ( ) return config
8,478
https://github.com/lambdalisue/notify/blob/1b6d7d1faa2cea13bfaa1f35130f279a0115e686/src/notify/conf.py#L102-L121
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Return True if data container has multiple timesteps .
def has_multiple_timesteps ( data ) : if "timestep" in data . keys ( ) : if len ( np . unique ( data [ "timestep" ] ) ) > 1 : return True return False
8,479
https://github.com/geophysics-ubonn/reda/blob/46a939729e40c7c4723315c03679c40761152e9e/lib/reda/utils/helper_functions.py#L83-L88
[ "def", "clean", "(", "self", ")", ":", "if", "self", ".", "_initialized", ":", "logger", ".", "info", "(", "\"brace yourselves, removing %r\"", ",", "self", ".", "path", ")", "shutil", ".", "rmtree", "(", "self", ".", "path", ")" ]
Split data into multiple timesteps .
def split_timesteps ( data , consistent_abmn = False ) : if has_multiple_timesteps ( data ) : grouped = data . groupby ( "timestep" ) return [ group [ 1 ] for group in grouped ] else : return data
8,480
https://github.com/geophysics-ubonn/reda/blob/46a939729e40c7c4723315c03679c40761152e9e/lib/reda/utils/helper_functions.py#L90-L96
[ "def", "arcball_constrain_to_axis", "(", "point", ",", "axis", ")", ":", "v", "=", "np", ".", "array", "(", "point", ",", "dtype", "=", "np", ".", "float64", ",", "copy", "=", "True", ")", "a", "=", "np", ".", "array", "(", "axis", ",", "dtype", "=", "np", ".", "float64", ",", "copy", "=", "True", ")", "v", "-=", "a", "*", "np", ".", "dot", "(", "a", ",", "v", ")", "# on plane", "n", "=", "vector_norm", "(", "v", ")", "if", "n", ">", "_EPS", ":", "if", "v", "[", "2", "]", "<", "0.0", ":", "np", ".", "negative", "(", "v", ",", "v", ")", "v", "/=", "n", "return", "v", "if", "a", "[", "2", "]", "==", "1.0", ":", "return", "np", ".", "array", "(", "[", "1.0", ",", "0.0", ",", "0.0", "]", ")", "return", "unit_vector", "(", "[", "-", "a", "[", "1", "]", ",", "a", "[", "0", "]", ",", "0.0", "]", ")" ]
Parses input text matches and replaces using avrodict
def parse ( text ) : # Sanitize text case to meet phonetic comparison standards fixed_text = validate . fix_string_case ( utf ( text ) ) # prepare output list output = [ ] # cursor end point cur_end = 0 # iterate through input text for cur , i in enumerate ( fixed_text ) : # Trap characters with unicode encoding errors try : i . encode ( 'utf-8' ) except UnicodeDecodeError : uni_pass = False else : uni_pass = True # Default value for match match = { 'matched' : False } # Check cur is greater than or equals cur_end. If cursor is in # a position that has alread been processed/replaced, we don't # process anything at all if not uni_pass : cur_end = cur + 1 output . append ( i ) elif cur >= cur_end and uni_pass : # Try looking in non rule patterns with current string portion match = match_non_rule_patterns ( fixed_text , cur ) # Check if non rule patterns have matched if match [ "matched" ] : output . append ( match [ "replaced" ] ) cur_end = cur + len ( match [ "found" ] ) else : # if non rule patterns have not matched, try rule patterns match = match_rule_patterns ( fixed_text , cur ) # Check if rule patterns have matched if match [ "matched" ] : # Update cur_end as cursor + length of match found cur_end = cur + len ( match [ "found" ] ) # Process its rules replaced = process_rules ( rules = match [ "rules" ] , fixed_text = fixed_text , cur = cur , cur_end = cur_end ) # If any rules match, output replacement from the # rule, else output it's default top-level/default # replacement if replaced is not None : # Rule has matched output . append ( replaced ) else : # No rules have matched # output common match output . append ( match [ "replaced" ] ) # If none matched, append present cursor value if not match [ "matched" ] : cur_end = cur + 1 output . append ( i ) # End looping through input text and produce output return '' . join ( output )
8,481
https://github.com/kaustavdm/pyAvroPhonetic/blob/26b7d567d8db025f2cac4de817e716390d7ac337/pyavrophonetic/avro.py#L38-L109
[ "def", "_wrapper", "(", "func", ",", "*", "args", ",", "*", "*", "kwargs", ")", ":", "try", ":", "if", "func", ".", "__name__", "==", "\"init\"", ":", "# init may not fail, as its return code is just stored as", "# private_data field of struct fuse_context", "return", "func", "(", "*", "args", ",", "*", "*", "kwargs", ")", "or", "0", "else", ":", "try", ":", "return", "func", "(", "*", "args", ",", "*", "*", "kwargs", ")", "or", "0", "except", "OSError", "as", "e", ":", "if", "e", ".", "errno", ">", "0", ":", "log", ".", "debug", "(", "\"FUSE operation %s raised a %s, returning errno %s.\"", ",", "func", ".", "__name__", ",", "type", "(", "e", ")", ",", "e", ".", "errno", ",", "exc_info", "=", "True", ")", "return", "-", "e", ".", "errno", "else", ":", "log", ".", "error", "(", "\"FUSE operation %s raised an OSError with negative \"", "\"errno %s, returning errno.EINVAL.\"", ",", "func", ".", "__name__", ",", "e", ".", "errno", ",", "exc_info", "=", "True", ")", "return", "-", "errno", ".", "EINVAL", "except", "Exception", ":", "log", ".", "error", "(", "\"Uncaught exception from FUSE operation %s, \"", "\"returning errno.EINVAL.\"", ",", "func", ".", "__name__", ",", "exc_info", "=", "True", ")", "return", "-", "errno", ".", "EINVAL", "except", "BaseException", "as", "e", ":", "self", ".", "__critical_exception", "=", "e", "log", ".", "critical", "(", "\"Uncaught critical exception from FUSE operation %s, aborting.\"", ",", "func", ".", "__name__", ",", "exc_info", "=", "True", ")", "# the raised exception (even SystemExit) will be caught by FUSE", "# potentially causing SIGSEGV, so tell system to stop/interrupt FUSE", "fuse_exit", "(", ")", "return", "-", "errno", ".", "EFAULT" ]
Matches given text at cursor position with non rule patterns
def match_non_rule_patterns ( fixed_text , cur = 0 ) : pattern = exact_find_in_pattern ( fixed_text , cur , NON_RULE_PATTERNS ) if len ( pattern ) > 0 : return { "matched" : True , "found" : pattern [ 0 ] [ 'find' ] , "replaced" : pattern [ 0 ] [ 'replace' ] } else : return { "matched" : False , "found" : None , "replaced" : fixed_text [ cur ] }
8,482
https://github.com/kaustavdm/pyAvroPhonetic/blob/26b7d567d8db025f2cac4de817e716390d7ac337/pyavrophonetic/avro.py#L111-L128
[ "def", "set_USRdict", "(", "self", ",", "USRdict", "=", "{", "}", ")", ":", "self", ".", "_check_inputs", "(", "USRdict", "=", "USRdict", ")", "self", ".", "_USRdict", "=", "USRdict" ]
Matches given text at cursor position with rule patterns
def match_rule_patterns ( fixed_text , cur = 0 ) : pattern = exact_find_in_pattern ( fixed_text , cur , RULE_PATTERNS ) # if len(pattern) == 1: if len ( pattern ) > 0 : return { "matched" : True , "found" : pattern [ 0 ] [ 'find' ] , "replaced" : pattern [ 0 ] [ 'replace' ] , "rules" : pattern [ 0 ] [ 'rules' ] } else : return { "matched" : False , "found" : None , "replaced" : fixed_text [ cur ] , "rules" : None }
8,483
https://github.com/kaustavdm/pyAvroPhonetic/blob/26b7d567d8db025f2cac4de817e716390d7ac337/pyavrophonetic/avro.py#L130-L149
[ "def", "set_USRdict", "(", "self", ",", "USRdict", "=", "{", "}", ")", ":", "self", ".", "_check_inputs", "(", "USRdict", "=", "USRdict", ")", "self", ".", "_USRdict", "=", "USRdict" ]
Returns pattern items that match given text cur position and pattern
def exact_find_in_pattern ( fixed_text , cur = 0 , patterns = PATTERNS ) : return [ x for x in patterns if ( cur + len ( x [ 'find' ] ) <= len ( fixed_text ) ) and x [ 'find' ] == fixed_text [ cur : ( cur + len ( x [ 'find' ] ) ) ] ]
8,484
https://github.com/kaustavdm/pyAvroPhonetic/blob/26b7d567d8db025f2cac4de817e716390d7ac337/pyavrophonetic/avro.py#L151-L154
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Process rules matched in pattern and returns suitable replacement
def process_rules ( rules , fixed_text , cur = 0 , cur_end = 1 ) : replaced = '' # iterate through rules for rule in rules : matched = False # iterate through matches for match in rule [ 'matches' ] : matched = process_match ( match , fixed_text , cur , cur_end ) # Break out of loop if we dont' have a match. Here we are # trusting avrodict to have listed matches sequentially if not matched : break # If a match is found, stop looping through rules any further if matched : replaced = rule [ 'replace' ] break # if any match has been found return replace value if matched : return replaced else : return None
8,485
https://github.com/kaustavdm/pyAvroPhonetic/blob/26b7d567d8db025f2cac4de817e716390d7ac337/pyavrophonetic/avro.py#L156-L183
[ "def", "remove_armor", "(", "armored_data", ")", ":", "stream", "=", "io", ".", "BytesIO", "(", "armored_data", ")", "lines", "=", "stream", ".", "readlines", "(", ")", "[", "3", ":", "-", "1", "]", "data", "=", "base64", ".", "b64decode", "(", "b''", ".", "join", "(", "lines", ")", ")", "payload", ",", "checksum", "=", "data", "[", ":", "-", "3", "]", ",", "data", "[", "-", "3", ":", "]", "assert", "util", ".", "crc24", "(", "payload", ")", "==", "checksum", "return", "payload" ]
Processes a single match in rules
def process_match ( match , fixed_text , cur , cur_end ) : # Set our tools # -- Initial/default value for replace replace = True # -- Set check cursor depending on match['type'] if match [ 'type' ] == 'prefix' : chk = cur - 1 else : # suffix chk = cur_end # -- Set scope based on whether scope is negative if match [ 'scope' ] . startswith ( '!' ) : scope = match [ 'scope' ] [ 1 : ] negative = True else : scope = match [ 'scope' ] negative = False # Let the matching begin # -- Punctuations if scope == 'punctuation' : # Conditions: XORd with negative if ( not ( ( chk < 0 and match [ 'type' ] == 'prefix' ) or ( chk >= len ( fixed_text ) and match [ 'type' ] == 'suffix' ) or validate . is_punctuation ( fixed_text [ chk ] ) ) ^ negative ) : replace = False # -- Vowels -- Checks: 1. Cursor should not be at first character # -- if prefix or last character if suffix, 2. Character at chk # -- should be a vowel. 3. 'negative' will invert the value of 1 # -- AND 2 elif scope == 'vowel' : if ( not ( ( ( chk >= 0 and match [ 'type' ] == 'prefix' ) or ( chk < len ( fixed_text ) and match [ 'type' ] == 'suffix' ) ) and validate . is_vowel ( fixed_text [ chk ] ) ) ^ negative ) : replace = False # -- Consonants -- Checks: 1. Cursor should not be at first # -- character if prefix or last character if suffix, 2. Character # -- at chk should be a consonant. 3. 'negative' will invert the # -- value of 1 AND 2 elif scope == 'consonant' : if ( not ( ( ( chk >= 0 and match [ 'type' ] == 'prefix' ) or ( chk < len ( fixed_text ) and match [ 'type' ] == 'suffix' ) ) and validate . is_consonant ( fixed_text [ chk ] ) ) ^ negative ) : replace = False # -- Exacts elif scope == 'exact' : # Prepare cursor for exact search if match [ 'type' ] == 'prefix' : exact_start = cur - len ( match [ 'value' ] ) exact_end = cur else : # suffix exact_start = cur_end exact_end = cur_end + len ( match [ 'value' ] ) # Validate exact find. if not validate . is_exact ( match [ 'value' ] , fixed_text , exact_start , exact_end , negative ) : replace = False # Return replace, which will be true if none of the checks above match return replace
8,486
https://github.com/kaustavdm/pyAvroPhonetic/blob/26b7d567d8db025f2cac4de817e716390d7ac337/pyavrophonetic/avro.py#L185-L248
[ "def", "normaliseURL", "(", "url", ")", ":", "url", "=", "unicode_safe", "(", "url", ")", ".", "strip", "(", ")", "# XXX: brutal hack", "url", "=", "unescape", "(", "url", ")", "pu", "=", "list", "(", "urlparse", "(", "url", ")", ")", "segments", "=", "pu", "[", "2", "]", ".", "split", "(", "'/'", ")", "while", "segments", "and", "segments", "[", "0", "]", "in", "(", "''", ",", "'..'", ")", ":", "del", "segments", "[", "0", "]", "pu", "[", "2", "]", "=", "'/'", "+", "'/'", ".", "join", "(", "segments", ")", "# remove leading '&' from query", "if", "pu", "[", "4", "]", ".", "startswith", "(", "'&'", ")", ":", "pu", "[", "4", "]", "=", "pu", "[", "4", "]", "[", "1", ":", "]", "# remove anchor", "pu", "[", "5", "]", "=", "\"\"", "return", "urlunparse", "(", "pu", ")" ]
Command - line interface for interacting with a WVA device
def cli ( ctx , hostname , username , password , config_dir , https ) : ctx . is_root = True ctx . user_values_entered = False ctx . config_dir = os . path . abspath ( os . path . expanduser ( config_dir ) ) ctx . config = load_config ( ctx ) ctx . hostname = hostname ctx . username = username ctx . password = password ctx . https = https # Creating the WVA object is deferred as some commands like clearconfig # should not require a username/password to perform them ctx . wva = None
8,487
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/cli.py#L110-L123
[ "def", "_MultiNotifyQueue", "(", "self", ",", "queue", ",", "notifications", ",", "mutation_pool", "=", "None", ")", ":", "notification_list", "=", "[", "]", "now", "=", "rdfvalue", ".", "RDFDatetime", ".", "Now", "(", ")", "for", "notification", "in", "notifications", ":", "if", "not", "notification", ".", "first_queued", ":", "notification", ".", "first_queued", "=", "(", "self", ".", "frozen_timestamp", "or", "rdfvalue", ".", "RDFDatetime", ".", "Now", "(", ")", ")", "else", ":", "diff", "=", "now", "-", "notification", ".", "first_queued", "if", "diff", ".", "seconds", ">=", "self", ".", "notification_expiry_time", ":", "# This notification has been around for too long, we drop it.", "logging", ".", "debug", "(", "\"Dropping notification: %s\"", ",", "str", "(", "notification", ")", ")", "continue", "notification_list", ".", "append", "(", "notification", ")", "mutation_pool", ".", "CreateNotifications", "(", "self", ".", "GetNotificationShard", "(", "queue", ")", ",", "notification_list", ")" ]
Perform an HTTP GET of the provided URI
def get ( ctx , uri ) : http_client = get_wva ( ctx ) . get_http_client ( ) cli_pprint ( http_client . get ( uri ) )
8,488
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/cli.py#L161-L196
[ "def", "write", "(", "self", ",", "basename", "=", "None", ",", "write_separate_manifests", "=", "True", ")", ":", "self", ".", "check_files", "(", ")", "n", "=", "0", "for", "manifest", "in", "self", ".", "partition_dumps", "(", ")", ":", "dumpbase", "=", "\"%s%05d\"", "%", "(", "basename", ",", "n", ")", "dumpfile", "=", "\"%s.%s\"", "%", "(", "dumpbase", ",", "self", ".", "format", ")", "if", "(", "write_separate_manifests", ")", ":", "manifest", ".", "write", "(", "basename", "=", "dumpbase", "+", "'.xml'", ")", "if", "(", "self", ".", "format", "==", "'zip'", ")", ":", "self", ".", "write_zip", "(", "manifest", ".", "resources", ",", "dumpfile", ")", "elif", "(", "self", ".", "format", "==", "'warc'", ")", ":", "self", ".", "write_warc", "(", "manifest", ".", "resources", ",", "dumpfile", ")", "else", ":", "raise", "DumpError", "(", "\"Unknown dump format requested (%s)\"", "%", "(", "self", ".", "format", ")", ")", "n", "+=", "1", "self", ".", "logger", ".", "info", "(", "\"Wrote %d dump files\"", "%", "(", "n", ")", ")", "return", "(", "n", ")" ]
DELETE the specified URI
def delete ( ctx , uri ) : http_client = get_wva ( ctx ) . get_http_client ( ) cli_pprint ( http_client . delete ( uri ) )
8,489
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/cli.py#L202-L217
[ "async", "def", "_sem_crawl", "(", "self", ",", "sem", ",", "res", ")", ":", "async", "with", "sem", ":", "st_", "=", "await", "self", ".", "crawl_raw", "(", "res", ")", "if", "st_", ":", "self", ".", "result", "[", "'ok'", "]", "+=", "1", "else", ":", "self", ".", "result", "[", "'fail'", "]", "+=", "1", "# take a little gap", "await", "asyncio", ".", "sleep", "(", "random", ".", "randint", "(", "0", ",", "1", ")", ")" ]
POST file data to a specific URI
def post ( ctx , uri , input_file ) : http_client = get_wva ( ctx ) . get_http_client ( ) cli_pprint ( http_client . post ( uri , input_file . read ( ) ) )
8,490
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/cli.py#L224-L231
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Sample the value of a vehicle data element
def sample ( ctx , element , timestamp , repeat , delay ) : element = get_wva ( ctx ) . get_vehicle_data_element ( element ) for i in xrange ( repeat ) : curval = element . sample ( ) if timestamp : print ( "{} at {}" . format ( curval . value , curval . timestamp . ctime ( ) ) ) else : print ( "{}" . format ( curval . value ) ) if i + 1 < repeat : # do not delay on last iteration time . sleep ( delay )
8,491
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/cli.py#L293-L330
[ "def", "get_all_indices", "(", "self", ",", "n_samples", "=", "None", ",", "max_samples", "=", "None", ",", "random_state", "=", "None", ")", ":", "if", "self", ".", "_indices_state", "is", "None", "and", "random_state", "is", "None", ":", "raise", "ValueError", "(", "'The program has not been evaluated for fitness '", "'yet, indices not available.'", ")", "if", "n_samples", "is", "not", "None", "and", "self", ".", "_n_samples", "is", "None", ":", "self", ".", "_n_samples", "=", "n_samples", "if", "max_samples", "is", "not", "None", "and", "self", ".", "_max_samples", "is", "None", ":", "self", ".", "_max_samples", "=", "max_samples", "if", "random_state", "is", "not", "None", "and", "self", ".", "_indices_state", "is", "None", ":", "self", ".", "_indices_state", "=", "random_state", ".", "get_state", "(", ")", "indices_state", "=", "check_random_state", "(", "None", ")", "indices_state", ".", "set_state", "(", "self", ".", "_indices_state", ")", "not_indices", "=", "sample_without_replacement", "(", "self", ".", "_n_samples", ",", "self", ".", "_n_samples", "-", "self", ".", "_max_samples", ",", "random_state", "=", "indices_state", ")", "sample_counts", "=", "np", ".", "bincount", "(", "not_indices", ",", "minlength", "=", "self", ".", "_n_samples", ")", "indices", "=", "np", ".", "where", "(", "sample_counts", "==", "0", ")", "[", "0", "]", "return", "indices", ",", "not_indices" ]
List short name of all current subscriptions
def list ( ctx ) : wva = get_wva ( ctx ) for subscription in wva . get_subscriptions ( ) : print ( subscription . short_name )
8,492
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/cli.py#L344-L348
[ "def", "_readWMSDatasets", "(", "self", ",", "datasetCards", ",", "directory", ",", "session", ",", "spatial", "=", "False", ",", "spatialReferenceID", "=", "4236", ")", ":", "if", "self", ".", "mapType", "in", "self", ".", "MAP_TYPES_SUPPORTED", ":", "# Get Mask Map dependency", "maskMap", "=", "session", ".", "query", "(", "RasterMapFile", ")", ".", "filter", "(", "RasterMapFile", ".", "projectFile", "==", "self", ")", ".", "filter", "(", "RasterMapFile", ".", "fileExtension", "==", "'msk'", ")", ".", "one", "(", ")", "for", "card", "in", "self", ".", "projectCards", ":", "if", "(", "card", ".", "name", "in", "datasetCards", ")", "and", "self", ".", "_noneOrNumValue", "(", "card", ".", "value", ")", ":", "# Get filename from project file", "filename", "=", "card", ".", "value", ".", "strip", "(", "'\"'", ")", "path", "=", "os", ".", "path", ".", "join", "(", "directory", ",", "filename", ")", "if", "os", ".", "path", ".", "isfile", "(", "path", ")", ":", "wmsDatasetFile", "=", "WMSDatasetFile", "(", ")", "wmsDatasetFile", ".", "projectFile", "=", "self", "wmsDatasetFile", ".", "read", "(", "directory", "=", "directory", ",", "filename", "=", "filename", ",", "session", "=", "session", ",", "maskMap", "=", "maskMap", ",", "spatial", "=", "spatial", ",", "spatialReferenceID", "=", "spatialReferenceID", ")", "else", ":", "self", ".", "_readBatchOutputForFile", "(", "directory", ",", "WMSDatasetFile", ",", "filename", ",", "session", ",", "spatial", ",", "spatialReferenceID", ",", "maskMap", "=", "maskMap", ")" ]
Delete a specific subscription by short name
def delete ( ctx , short_name ) : wva = get_wva ( ctx ) subscription = wva . get_subscription ( short_name ) subscription . delete ( )
8,493
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/cli.py#L354-L358
[ "def", "enforce_filetype_file", "(", "form", ",", "field", ")", ":", "if", "form", ".", "_fields", ".", "get", "(", "'filetype'", ")", ".", "data", "!=", "RESOURCE_FILETYPE_FILE", ":", "return", "domain", "=", "urlparse", "(", "field", ".", "data", ")", ".", "netloc", "allowed_domains", "=", "current_app", ".", "config", "[", "'RESOURCES_FILE_ALLOWED_DOMAINS'", "]", "allowed_domains", "+=", "[", "current_app", ".", "config", ".", "get", "(", "'SERVER_NAME'", ")", "]", "if", "current_app", ".", "config", ".", "get", "(", "'CDN_DOMAIN'", ")", ":", "allowed_domains", ".", "append", "(", "current_app", ".", "config", "[", "'CDN_DOMAIN'", "]", ")", "if", "'*'", "in", "allowed_domains", ":", "return", "if", "domain", "and", "domain", "not", "in", "allowed_domains", ":", "message", "=", "_", "(", "'Domain \"{domain}\" not allowed for filetype \"{filetype}\"'", ")", "raise", "validators", ".", "ValidationError", "(", "message", ".", "format", "(", "domain", "=", "domain", ",", "filetype", "=", "RESOURCE_FILETYPE_FILE", ")", ")" ]
Remove all registered subscriptions
def clear ( ctx ) : wva = get_wva ( ctx ) for subscription in wva . get_subscriptions ( ) : sys . stdout . write ( "Deleting {}... " . format ( subscription . short_name ) ) sys . stdout . flush ( ) subscription . delete ( ) print ( "Done" )
8,494
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/cli.py#L363-L383
[ "def", "waveform_stack", "(", "mediafiles", ",", "xy_size", ",", "output", "=", "None", ",", "label_style", "=", "None", ",", "center_color", "=", "None", ",", "outer_color", "=", "None", ",", "bg_color", "=", "None", ")", ":", "img_files", "=", "[", "]", "output", "=", "output", "or", "os", ".", "path", ".", "abspath", "(", "os", ".", "path", ".", "dirname", "(", "os", ".", "path", ".", "commonprefix", "(", "mediafiles", ")", ")", ")", "if", "os", ".", "path", ".", "isdir", "(", "output", ")", ":", "output", "=", "os", ".", "path", ".", "join", "(", "output", ",", "\"waveforms.jpg\"", ")", "cmd", "=", "[", "config", ".", "CMD_IM_MONTAGE", "]", "+", "shlex", ".", "split", "(", "label_style", "or", "WAVE_LABEL_STYLE", ")", "cmd", "+=", "[", "\"-tile\"", ",", "\"1x%d\"", "%", "len", "(", "mediafiles", ")", ",", "\"-geometry\"", ",", "\"%dx%d\"", "%", "xy_size", ",", "\"-label\"", ",", "\"%t\"", "]", "try", ":", "tempdir", "=", "tempfile", ".", "mktemp", "(", "__name__", ")", "os", ".", "makedirs", "(", "tempdir", ")", "for", "mediafile", "in", "sorted", "(", "mediafiles", ")", ":", "img_files", ".", "append", "(", "waveform_image", "(", "mediafile", ",", "xy_size", ",", "tempdir", ",", "center_color", ",", "outer_color", ",", "bg_color", ")", ")", "cmd", ".", "extend", "(", "img_files", ")", "cmd", ".", "append", "(", "output", ")", "subprocess", ".", "check_call", "(", "cmd", ",", "stdout", "=", "open", "(", "os", ".", "devnull", ",", "\"wb\"", ")", ",", "stderr", "=", "subprocess", ".", "STDOUT", ")", "finally", ":", "if", "os", ".", "path", ".", "isdir", "(", "tempdir", ")", ":", "shutil", ".", "rmtree", "(", "tempdir", ",", "ignore_errors", "=", "True", ")", "return", "output" ]
Show metadata for a specific subscription
def show ( ctx , short_name ) : wva = get_wva ( ctx ) subscription = wva . get_subscription ( short_name ) cli_pprint ( subscription . get_metadata ( ) )
8,495
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/cli.py#L389-L400
[ "def", "_incomplete_files", "(", "filenames", ")", ":", "tmp_files", "=", "[", "get_incomplete_path", "(", "f", ")", "for", "f", "in", "filenames", "]", "try", ":", "yield", "tmp_files", "for", "tmp", ",", "output", "in", "zip", "(", "tmp_files", ",", "filenames", ")", ":", "tf", ".", "io", ".", "gfile", ".", "rename", "(", "tmp", ",", "output", ")", "finally", ":", "for", "tmp", "in", "tmp_files", ":", "if", "tf", ".", "io", ".", "gfile", ".", "exists", "(", "tmp", ")", ":", "tf", ".", "io", ".", "gfile", ".", "remove", "(", "tmp", ")" ]
Add a subscription with a given short_name for a given uri
def add ( ctx , short_name , uri , interval , buffer ) : wva = get_wva ( ctx ) subscription = wva . get_subscription ( short_name ) subscription . create ( uri , buffer , interval )
8,496
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/cli.py#L409-L432
[ "def", "merge_cts_records", "(", "file_name", ",", "crypto_idfp", ",", "crypto_idfps", ")", ":", "db", "=", "XonoticDB", ".", "load_path", "(", "file_name", ")", "db", ".", "merge_cts_records", "(", "crypto_idfp", ",", "crypto_idfps", ")", "db", ".", "save", "(", "file_name", ")" ]
Output the contents of the WVA event stream
def listen ( ctx ) : wva = get_wva ( ctx ) es = wva . get_event_stream ( ) def cb ( event ) : cli_pprint ( event ) es . add_event_listener ( cb ) es . enable ( ) while True : time . sleep ( 5 )
8,497
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/cli.py#L437-L473
[ "def", "multicomp", "(", "pvals", ",", "alpha", "=", "0.05", ",", "method", "=", "'holm'", ")", ":", "if", "not", "isinstance", "(", "pvals", ",", "(", "list", ",", "np", ".", "ndarray", ")", ")", ":", "err", "=", "\"pvals must be a list or a np.ndarray\"", "raise", "ValueError", "(", "err", ")", "if", "method", ".", "lower", "(", ")", "in", "[", "'b'", ",", "'bonf'", ",", "'bonferroni'", "]", ":", "reject", ",", "pvals_corrected", "=", "bonf", "(", "pvals", ",", "alpha", "=", "alpha", ")", "elif", "method", ".", "lower", "(", ")", "in", "[", "'h'", ",", "'holm'", "]", ":", "reject", ",", "pvals_corrected", "=", "holm", "(", "pvals", ",", "alpha", "=", "alpha", ")", "elif", "method", ".", "lower", "(", ")", "in", "[", "'fdr'", ",", "'fdr_bh'", "]", ":", "reject", ",", "pvals_corrected", "=", "fdr", "(", "pvals", ",", "alpha", "=", "alpha", ",", "method", "=", "'fdr_bh'", ")", "elif", "method", ".", "lower", "(", ")", "in", "[", "'fdr_by'", "]", ":", "reject", ",", "pvals_corrected", "=", "fdr", "(", "pvals", ",", "alpha", "=", "alpha", ",", "method", "=", "'fdr_by'", ")", "elif", "method", ".", "lower", "(", ")", "==", "'none'", ":", "pvals_corrected", "=", "pvals", "with", "np", ".", "errstate", "(", "invalid", "=", "'ignore'", ")", ":", "reject", "=", "np", ".", "less", "(", "pvals_corrected", ",", "alpha", ")", "else", ":", "raise", "ValueError", "(", "'Multiple comparison method not recognized'", ")", "return", "reject", ",", "pvals_corrected" ]
Present a live graph of the incoming streaming data
def graph ( ctx , items , seconds , ylim ) : wva = get_wva ( ctx ) es = wva . get_event_stream ( ) try : from wva import grapher except ImportError : print ( "Unable to graph... you must have matplotlib installed" ) else : stream_grapher = grapher . WVAStreamGrapher ( wva , items , seconds = seconds , ylim = ylim ) es . enable ( ) stream_grapher . run ( )
8,498
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/cli.py#L481-L507
[ "def", "transform_i_to_j_optional", "(", "self", ",", "line", ":", "str", ")", "->", "str", ":", "words", "=", "line", ".", "split", "(", "\" \"", ")", "space_list", "=", "string_utils", ".", "space_list", "(", "line", ")", "corrected_words", "=", "[", "]", "for", "word", "in", "words", ":", "found", "=", "False", "for", "prefix", "in", "self", ".", "constants", ".", "PREFIXES", ":", "if", "word", ".", "startswith", "(", "prefix", ")", "and", "word", "!=", "prefix", ":", "corrected_words", ".", "append", "(", "self", ".", "syllabifier", ".", "convert_consonantal_i", "(", "prefix", ")", ")", "corrected_words", ".", "append", "(", "self", ".", "syllabifier", ".", "convert_consonantal_i", "(", "word", "[", "len", "(", "prefix", ")", ":", "]", ")", ")", "found", "=", "True", "break", "if", "not", "found", ":", "corrected_words", ".", "append", "(", "self", ".", "syllabifier", ".", "convert_consonantal_i", "(", "word", ")", ")", "new_line", "=", "string_utils", ".", "join_syllables_spaces", "(", "corrected_words", ",", "space_list", ")", "# the following two may be tunable and subject to improvement", "char_list", "=", "string_utils", ".", "overwrite", "(", "list", "(", "new_line", ")", ",", "\"[bcdfgjkmpqrstvwxzBCDFGHJKMPQRSTVWXZ][i][{}]\"", ".", "format", "(", "self", ".", "constants", ".", "VOWELS_WO_I", ")", ",", "\"j\"", ",", "1", ")", "char_list", "=", "string_utils", ".", "overwrite", "(", "char_list", ",", "\"[{}][iI][{}]\"", ".", "format", "(", "self", ".", "constants", ".", "LIQUIDS", ",", "self", ".", "constants", ".", "VOWELS_WO_I", ")", ",", "\"j\"", ",", "1", ")", "return", "\"\"", ".", "join", "(", "char_list", ")" ]
Enable ssh login as the Python user for the current user
def authorize ( ctx , public_key , append ) : wva = get_wva ( ctx ) http_client = wva . get_http_client ( ) authorized_keys_uri = "/files/userfs/WEB/python/.ssh/authorized_keys" authorized_key_contents = public_key if append : try : existing_contents = http_client . get ( authorized_keys_uri ) authorized_key_contents = "{}\n{}" . format ( existing_contents , public_key ) except WVAHttpNotFoundError : pass # file doesn't exist, just write the public key http_client . put ( authorized_keys_uri , authorized_key_contents ) print ( "Public key written to authorized_keys for python user." ) print ( "You should now be able to ssh to the device by doing the following:" ) print ( "" ) print ( " $ ssh python@{}" . format ( get_root_ctx ( ctx ) . hostname ) )
8,499
https://github.com/digidotcom/python-wvalib/blob/4252735e2775f80ebaffd813fbe84046d26906b3/wva/cli.py#L523-L546
[ "def", "parse_torrent_properties", "(", "table_datas", ")", ":", "output", "=", "{", "'category'", ":", "table_datas", "[", "0", "]", ".", "text", ",", "'subcategory'", ":", "None", ",", "'quality'", ":", "None", ",", "'language'", ":", "None", "}", "for", "i", "in", "range", "(", "1", ",", "len", "(", "table_datas", ")", ")", ":", "td", "=", "table_datas", "[", "i", "]", "url", "=", "td", ".", "get", "(", "'href'", ")", "params", "=", "Parser", ".", "get_params", "(", "url", ")", "if", "Parser", ".", "is_subcategory", "(", "params", ")", "and", "not", "output", "[", "'subcategory'", "]", ":", "output", "[", "'subcategory'", "]", "=", "td", ".", "text", "elif", "Parser", ".", "is_quality", "(", "params", ")", "and", "not", "output", "[", "'quality'", "]", ":", "output", "[", "'quality'", "]", "=", "td", ".", "text", "elif", "Parser", ".", "is_language", "(", "params", ")", "and", "not", "output", "[", "'language'", "]", ":", "output", "[", "'language'", "]", "=", "td", ".", "text", "return", "output" ]