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| SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object coalda.data.Reader coalda.data.ReadFromFile
public class ReadFromFile
| Nested Class Summary |
|---|
| Nested classes/interfaces inherited from class coalda.data.Reader |
|---|
Reader.InformationType |
| Field Summary | |
|---|---|
private java.io.BufferedReader |
br
Reader for file |
private int |
column
Cursor column |
private int |
currentRow
Cursor line. |
private java.lang.String[] |
dataColumns
|
private java.lang.String |
dataRow
Information that is imported at the moment |
private boolean |
fileOpen
File open successful |
private boolean |
isVector
True if it is a vector, false if it is a matrix |
private java.lang.String |
nextDataRow
|
private int |
readRows
|
| Fields inherited from class coalda.data.Reader |
|---|
calcID, infoType |
| Constructor Summary | |
|---|---|
ReadFromFile()
|
| Method Summary | |
|---|---|
void |
finalize()
Method finalize. |
boolean |
hasNextLine()
Method hasNextLine. |
boolean |
hasNextRow()
Method hasNextRow. |
boolean |
hasNextValue()
Method hasNextValue. |
java.lang.String[] |
nextLine()
Method nextLine. |
java.lang.String |
nextRow()
Method nextRow. |
java.lang.String |
nextValue()
Method hasNextValue. |
int |
numberOfValues()
Method numberOfValues. |
java.lang.String[] |
readCompleteVector(Reader.InformationType type)
Method readCompleteVector. |
private java.lang.String |
readLine()
Method readLine. |
void |
readLines(Reader.InformationType type,
java.lang.String fields,
java.lang.String condition)
Method readLines. |
void |
readMatrix(Reader.InformationType type)
Method readMatrix. |
void |
readVector(Reader.InformationType type)
Method readVector. |
| Methods inherited from class coalda.data.Reader |
|---|
readCompleteVector, readLines, readMatrix, readVector, setCalcID, setInformationType |
| Methods inherited from class java.lang.Object |
|---|
clone, equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Field Detail |
|---|
private java.lang.String dataRow
private java.lang.String nextDataRow
private java.lang.String[] dataColumns
private boolean fileOpen
private boolean isVector
private int currentRow
private int readRows
private int column
private java.io.BufferedReader br
| Constructor Detail |
|---|
public ReadFromFile()
| Method Detail |
|---|
public void readMatrix(Reader.InformationType type)
readMatrix
in class Reader
type
- Type of information to read.public void readVector(Reader.InformationType type)
readVector
in class Reader
type
- Type of information to read.public java.lang.String[] readCompleteVector(Reader.InformationType type)
readCompleteVector
in class Reader
type
- Type of information to read.
private java.lang.String readLine()
public boolean hasNextRow()
hasNextRow
in class Reader
public boolean hasNextValue()
hasNextValue
in class Reader
public java.lang.String nextRow()
nextRow
in class Reader
public java.lang.String nextValue()
nextValue
in class Reader
public int numberOfValues()
numberOfValues
in class Reader
public void readLines(Reader.InformationType type, java.lang.String fields, java.lang.String condition)
readLines
in class Reader
type
- Type of information to read.fields
- Columns of the data to be read.condition
- Condition returned lines must fulfill.public boolean hasNextLine()
hasNextLine
in class Reader
public java.lang.String[] nextLine()
nextLine
in class Reader
public void finalize()
finalize
in class Reader
|
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| PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
| SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |


ï»¿
Cuyahoga County Soldiers’ and Sailors’ Monument Commission
Notice of Names on the Wall Committee Meeting
Monday October 7, 2019
9:00AM
The Soldiersâ and Sailorsâ Monument Commission Name on the Wall Committee will meet on at 9:00am at the Interstate Plaza located at 16600 Sprague Road, Middleburg Heights, Ohio 44130
For the Commission
Timothy Daley
Executive Director
Cuyahoga County Soldiers’ and Sailors’ Monument Commission
Notice of Executive Committee Meeting
Tueday October 8, 2019
12:00 Noon
The Soldiersâ and Sailorsâ Monument Commission will meet on at 12:00 Noon at the Monument Showcase located at 401 Euclid Avenue, Suite 46, Cleveland Ohio 44114
216-621-3710
For the Commission
Timothy Daley
Executive Director
Cuyahoga County Soldiers’ and Sailors’ Monument Commission
Notice of Commission Meeting
Tueday October 15, 2019
6:00 PM
The Soldiersâ and Sailorsâ Monument Commission will meet on Tuesday , October 15, 2019 at 6:00PM at 3 Public Square, Cleveland Ohio 44114
216-621-3710
For the Commission
Timothy Daley
Executive Director
Copyright 2019. Cleveland Soldiers' and Sailors' Monument. All Rights Reserved.
Website Designed and Maintained by Ken Freshley


@* * Copyright 2021 HM Revenue & Customs * * Licensed under the Apache License, Version 2.0 (the "License"); * you may not use this file except in compliance with the License. * You may obtain a copy of the License at * * http://www.apache.org/licenses/LICENSE-2.0 * * Unless required by applicable law or agreed to in writing, software * distributed under the License is distributed on an "AS IS" BASIS, * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. * See the License for the specific language governing permissions and * limitations under the License. *@ @import config.AppConfig @import controllers.Tab @import controllers.routes.CreateCorrespondenceController @import helper._ @import models.{Case, CorrespondenceApplication} @import models.request.AuthenticatedRequest @import models.viewmodels.{CaseHeaderViewModel, NoTabSelected} @import views.html.components.confirm_or_cancel_buttons @import views.html.includes.main @import views.html.forms.components._ @import views.html.partials.{error_summary, back_link} @this(case_heading: views.html.v2.case_heading) @(c: Case, form : Form[Case])(implicit request: AuthenticatedRequest[_], messages: Messages, appConfig: AppConfig) @main(bodyClasses = None, customTitle = Some(messages("case.v2.correspondence.case-contact-edit-title")), customPrimaryNavTab = NoTabSelected) {


For Burton upon Trent, Staffordshire, which has a population of 80,000, which sits next to the River Trent is most famous for being the brewing capital of the world.
It is home to many a top firm too with the likes of Holland and Barrett, Waterstones and Clippers to name but a few.
It also has a football club in Burton Albion FC that punches above its weight given their exploits in the Championship for two seasons and reaching the semi-final of the league cup.
But Burtonians might be surprised to learn they are not alone as there are one or two other Burtons across the pond in America.
We've compiled a list of what we believe to be every place named Burton in the USA to see how they compare to our town – and some of them may surprise you.
Some cities which share our name may be bigger, but can they beat our beer?
So here are a few of the other Burtons in the world:
Places named Burton from around the world
-
Burton, Michigan
Burton is the second largest city in Genessee County in the state of Michigan, with a population of 29,999 - a lot less than half of our Burton population.
And just like our very own Burton, Burton, in Michigan is close to a place called Foremark.
The City of Burton was originally organised as Burton Township, named after John Burton, a prominent local farmer. Burton Township had first been a part of Grand Blanc Township in 1835 then Flint Township in 1836.
Just like East Midlands Airport, Burton Michigan boasts the Athelone Memorial Airport under 30 minutes away.
Burton, Michigan. Credit: Google
-
Burton, Illinois, an unincorporated community in Adams County
As of the 2010 census, its population was 909 and it contained 370 housing units.
Burton was created in 1836. A post office called Burton was established in 1840, and remained in operation until 1922.
The township of Burton and Adams County contains five cemeteries: Burton, Independence, Kimmons, Newton and Tandy. This can be compared to our local Stapenhill Cemetery.
Burton, Illinois. Credit: Google
-
Burton Township, Mchenry County, Illinois
Burton Township is the smallest in area in McHenry County, Illinois. As of the 2010 census, its population was 5,003 and it contained 1,758 housing units.
The English first settled in Burton Township in 1836, and the name English Prairie was given it. Later settlers called the township Benton, but after learning that there was already a post office and township of Benton in Illinois, the name was changed to Burton on December 28, 1850
It boasts Richardson Adventure Farm with the world's largest corn maze - a little bit like our National Forest Adventure Farm.
Burton, Illinois. Credit: Google
-
Burton Township, Yellow Medicine County, Minnesota
Burton Township was created in 1879, and named after Burton French, the father of a first settler.
As of the census of of 2000, there were 174 people, 65 households, and 46 families residing in the township. The racial makeup of the township was 100 per cent white.
It boasts the Burton Lake - a little bit smaller than our beloved River Trent.
Burton, Minnesota. Credit: Google
-
Burton, Missouri
A post office called Burton was established in 1873, and remained in operation until 1935. The community has the name of Prior Burton, the original owner of the site.
Running through Burton is the Salt Fork stream - not as impressive at the River Trent though. It is also closed to the town of Ivanhoe - a name connected closely to our neighbouring town of Ashby.
Burton, Missouri. Credit: Google
-
Burton Township, Geauga County, Ohio
Burton Township is one of the sixteen townships of Geauga County, Ohio. Burton Township was established in 1806, and named after Titus Burton, the son of a first settler.
One of the more similar towns to us, this Burton even has the Burton Wetlands and the Burton Wetlands Nature Reserve which can be compared to our Washlands. Its river is the East Branch Cuyahoga River.
Burton, Ohio. Credit: Google
-
Burton, South Carolina, on Port Royal Island in Beaufort County
Port Royal Island, historically Port Royal, is an island located in Beaufort County, South Carolina. It is considered one of Sea Islands in the Lowcounty region.
Burton's heyday was during the truck farming era in Beaufort County from 1900 to 1930. The 'centre' of Burton was where Broad River Boulevard crosses the abandoned Port Royal Railroad tracks and Route 21.
Again, close to a water source of Salt Creek, Burton does boast some similarities to us and you may recognise some of its businesses such as Domino's, KFC and Enterprise Cars.
Burton, South Carolina. Credit: Google
-
Burton, Georgia: The town that lies underwater
Did you know that there was a Burton in America that is now covered by a lake? Burton, Georgia, was once a mighty town famous for "gold-rushing", where many would flock to the town to hunt for the precious metal.
A railway company went on to buy the whole town and decided to close the dam. Before long, the town of Burton became submerged underwater, and is now called Lake Burton.
Back here in Burton-on-Trent, The Washlands might be known for flooding as the Trent bursts its banks now and then - but so far our town has never ended up underwater - not even in the big flood of 2000!
Burton, Georgia. Credit: Google


--- layout: default title: AmazonSmile group: support group-weight: 3 permalink: /support/amazon-smile/ ---
Support OSM when you shop AmazonSmile, a special website operated by Amazon that makes donations to charitable organizations selected by its customers. It's easy. Visit the AmazonSmile website "http://smile.amazon.com" and enter "Orchestra Santa Monica" to specify our group as your recipient charity. Be sure to bookmark the AmazonSmile website, then do all of your Amazon shopping at AmazonSmile and OSM will receive 0.5% of your eligible purchases. :-)


Become of True Boracayan with Janvan, of Course
Typically you're doing the Freedom Trail walk in Boston. Why trudge along the busiest streets with
100's of other tourists. Start at Christopher Columbus Park in the North End. Walk along Atlantic Ave
and grab a coffee at any shop you see it doesn't matter. Walk down along the wharfs until you come to
the Zacum Bridge leading into Charlestown. Walk up to the Bunker Hill Monument, snap pictures -
look at the 18th century houses that line up like rows along the streets. Afterwards, walk down
Monument St. When you a sign for the Warren Tavern You've found your late lunch and beers -
Frequented by Paul Revere in the 1700's and still in operation today! Enjoy.
Typically you're doing the Freedom Trail walk in Boston. Why trudge along the busiest streets with
100's of other tourists. Start at Christopher Columbus Park in the North End. Walk along Atlantic Ave
and grab a coffee at any shop you see it doesn't matter. Walk down along the wharfs until you come to
the Zacum Bridge leading into Charlestown. Walk up to the Bunker Hill Monument, snap pictures -
look at the 18th century houses that line up like rows along the streets. Afterwards, walk down
Monument St. When you a sign for the Warren Tavern You've found your late lunch and beers -
Frequented by Paul Revere in the 1700's and still in operation today! Enjoy.
Typically you're doing the Freedom Trail walk in Boston. Why trudge along the busiest streets with
100's of other tourists. Start at Christopher Columbus Park in the North End. Walk along Atlantic Ave
and grab a coffee at any shop you see it doesn't matter. Walk down along the wharfs until you come to
the Zacum Bridge leading into Charlestown. Walk up to the Bunker Hill Monument, snap pictures -
look at the 18th century houses that line up like rows along the streets. Afterwards, walk down
Monument St. When you a sign for the Warren Tavern You've found your late lunch and beers -
Frequented by Paul Revere in the 1700's and still in operation today! Enjoy.


--- layout: default title: about Dmytro Yashkir ---
Love making stuff, coding, running, rockclimbig, beer, soccer. Trying to make everyone's phone into broadcast radio station at Instaradio.


Example to demonstrate PDF.js library usage with Browserify.
Build project and install the example dependencies:
$ gulp dist-install
$ cd examples/browserify
$ npm install
To build Browserify bundles, run gulp build
. If you are running
a web server, you can observe the build results at
http://localhost:8888/examples/browserify/index.html
See main.js, worker.js and gulpfile.js files. Please notice that PDF.js
packaging requires packaging of the main application and PDF.js worker code,
and the workerSrc
path shall be set to the latter file. The pdf.worker.js file
shall be excluded from the main bundle.
Alternatives to the gulp commands (without compression) are:
$ mkdir -p ../../build/browserify
$ node_modules/.bin/browserify main.js -u ./node_modules/pdfjs-dist/build/pdf.worker.js -o ../../build/browserify/main.bundle.js
$ node_modules/.bin/browserify worker.js -o ../../build/browserify/pdf.worker.bundle.js


Displays all parameters of all WebCL platforms and devices available on your system. So far this has only been tested with Samsung's WebCL prototype for WebKit and is known incompatible with Nokia's WebCL extension for Firefox.


"LogisticRegression.results"))) as f:
outstr = f.read()
logistic_result_score = float(
SCORE_OUTPUT_RE.search(outstr).groups()[0])
assert_almost_equal(logistic_result_score, 0.5)
outd = json.loads(f.read())
// logistic_result_score = float(
// SCORE_OUTPUT_RE.search(outstr).groups()[0])
logistic_result_score = outd[0]["score"]
assert_almost_equal(logistic_result_score, 0.5)


Robot localization is the task of the determining the position and orientation of a platform relative to the coordinate system of some environment. Fundamentally, localization is a coordinate system transformation task, as it is the process of estimating the relative orientation between a coordinate system fixed to the body of the platform and the environment's coordinate system. As robot pose cannot be sensed directly, multiple different sensor measurements are typically combined to estimate the robot's pose within a given environment.
Different Localization Problems
Different types of localization problems exist, subject to the availability of prior knowledge, sensor data, the nature of the environment, and the environment localization is performed with respect to.
The first distincition can be made between local and global localization problems, subject to the availability of initial data and incoming sensor data:
- Position Tracking: Position tracking is the task of estimating the variation in pose over time subject to a known initial pose. It is local localization problem as the uncertainty is confined to a region near the robot's true pose. Gaussian noise models are typically sufficient to approximate the posterior distribution.
- Global Localization: Global localization is the task of estimating the variation in pose over time subject to an unknown initial pose but a known map of the environment. No assumptions can be made regarding the boundness of the pose error, nor can any assumptions be made regarding the form of the posterior distribution.
- Kidnapped Robot Problem: The kidnapped robot problem is the task of estimating the variation in pose over time subject to both an unknown initial condition and an unknown map of the environment. This problem can be seen as the case in which a global localization algorithm fails, and the solution to this problem is a measure of how well an algorithm can recover from such a failure in practice
The next distinction can be made on the basis of a static or dynamic environment:
- Static Environments: The only variations are the robot's pose over time, and all other objects remain stationary
- Dynamic Environments: The location of objects in the environment other than the robot vary over time.
Another distinction relates to whether the localization algorithm is integrated into the robot's control system, or if it simply observes the control commands:
- Passive Localization: The localization algorithm is not integrated directly into the control system, and observes the issued control commands.
- Active Localization: Active localization algorithms are directly integrated into the robot's control system.
Localization can further be characterized on the basis of whether a single robot or multiple robots are used to estimate the pose of all robots simultaneously:
- Single-Robot Localization: All data is collected by a single platform.
- Multi-Robot Localization: Data is collected by multiple platforms, and the belief of one robot can be used to bias the belief of another robot when the relative location of the platforms is available, thereby increasing the accuracy of the overall pose estimates.
Markov Localization
Markov localization involves applying the Bayes filter to the localization problem. Markov localization transforms the belief state at epoch t-1 into the belief state at epoch t. This framework can be used to solve the tracking, global localization and kidnapped robot problem in a static enviornment. If an approximate initial pose is known, the algorithm is initialized with a narrow gaussian distribution centered around the belief state, whereas if the initial pose is unknown the algorithm is initialized with a uniform distribution over all valid poses within the environment.
EKF Localization
EKF localization represents the belief state based upon the mean state vector and the covariance matrix of the state estimate, in other words the first and second moments of the posterior distribution. EKF localization assumes a feature based map. In addition, EKF localization processes multiple sensor measurements simultaneously assuming conditional independence between the different measurements themselves. Maximum likelihood estimation can be used ot generate an optimal estimate for the correspondence variables ???, however they suffer from divergence when an invalid hypothesis for a given track is accepted as the best estimate. This issue can be addressed by selecting landmarks that are sufficiently unique and sufficiently far apart, in addition to techniques to insure that hte robot's pose uncertainty remains small. Further, outlier rejection techniques and knowledge of the robot's approximate location can be used to reject highly improbably landmark observations.
One limitation to the EKF is that it suffers from divergence when an incorrect hypothesis is selected, as it assumes a single unimodal gaussian posterior distribution. The multi-hypothesis tracking algorithm is one strategy in which the posterior distribution is represented by a Gaussian mixture model, and each hypothesis within the mixture is itself a Gaussian posterior estimate of the state. These different hypothesis are assigned a scalar mixture weight used to combine them into a final state estimate at each epoch. In theory this algorithm is computationally intractable, however several strategies can be employed to render both the EKF and MHT more efficient:
- Efficiently search methods for matching observed landmarks to those in the map
- Mutual Exclusivity between different observations and different landmarks. In other words, different features observed at the same time cannot correspond to the same landmark in the environment
- Outlier rejection strategies can also be used to increase the efficiency and robustness of the algorithm


cis_interface.drivers package¶
Subpackages¶
- cis_interface.drivers.tests package
- Submodules
- cis_interface.drivers.tests.test_CMakeModelDriver module
- cis_interface.drivers.tests.test_ClientDriver module
- cis_interface.drivers.tests.test_ClientResponseDriver module
- cis_interface.drivers.tests.test_ConnectionDriver module
- cis_interface.drivers.tests.test_Driver module
- cis_interface.drivers.tests.test_FileInputDriver module
- cis_interface.drivers.tests.test_FileOutputDriver module
- cis_interface.drivers.tests.test_GCCModelDriver module
- cis_interface.drivers.tests.test_LPyModelDriver module
- cis_interface.drivers.tests.test_MakeModelDriver module
- cis_interface.drivers.tests.test_MatlabModelDriver module
- cis_interface.drivers.tests.test_ModelDriver module
- cis_interface.drivers.tests.test_PythonModelDriver module
- cis_interface.drivers.tests.test_RMQAsyncClientDriver module
- cis_interface.drivers.tests.test_RMQAsyncServerDriver module
- cis_interface.drivers.tests.test_RMQClientDriver module
- cis_interface.drivers.tests.test_RMQServerDriver module
- cis_interface.drivers.tests.test_ServerDriver module
- cis_interface.drivers.tests.test_ServerResponseDriver module
- Module contents
Submodules¶
cis_interface.drivers.CMakeModelDriver module¶
-
class
cis_interface.drivers.CMakeModelDriver.
CMakeModelDriver
(name, args, preserve_cache=False, **kwargs)[source]¶ Bases:
cis_interface.drivers.ModelDriver.ModelDriver
Class for running cmake compiled drivers. Before running the cmake command, the cmake commands for setting the necessary compiler & linker flags for the interface’s C/C++ library are written to a file called ‘cis_cmake.txt’ that should be included in the CMakeLists.txt file (after the target executable has been added).
Parameters: - name (str) – Driver name.
- args (str, list) – Executable that should be created (cmake target) and any arguments for the executable.
- sourcedir (str, optional) – Source directory to call cmake on. If not provided it is set to self.working_dir. This should be the directory containing the CMakeLists.txt file. It can be relative to self.working_dir or absolute.
- builddir (str, optional) – Directory where the build should be saved. Defaults to <sourcedir>/build. It can be relative to self.working_dir or absolute.
- cmakeargs (list, optional) – Arguments that should be passed to cmake. Defaults to [].
- preserve_cache (bool, optional) – If True the cmake cache will be kept following the run, otherwise all files created by cmake will be cleaned up. Defaults to False.
- **kwargs – Additional keyword arguments are passed to parent class.
-
preserve_cache
¶ If True the cmake cache will be kept following the run, otherwise all files created by cmake will be cleaned up.
Type: bool
Raises: RuntimeError
– If neither the IPC or ZMQ C libraries are available.-
classmethod
is_installed
()[source]¶ Determine if this model driver is installed on the current machine.
Returns: - Truth of if this model driver can be run on the current
- machine.
Return type: bool
-
run_cmake
(target=None)[source]¶ Run the cmake command on the source.
Parameters: target (str, optional) – Target to build. Raises: RuntimeError
– If there is an error in running cmake.
-
cis_interface.drivers.CMakeModelDriver.
build_regex_win32
()[source]¶ Build the regex_win32 library using cmake.
cis_interface.drivers.ClientDriver module¶
-
class
cis_interface.drivers.ClientDriver.
ClientDriver
(model_request_name, request_name=None, comm=None, comm_address=None, **kwargs)[source]¶ Bases:
cis_interface.drivers.ClientRequestDriver.ClientRequestDriver
Alias for ClientRequestDriver.
cis_interface.drivers.ClientRequestDriver module¶
-
class
cis_interface.drivers.ClientRequestDriver.
ClientRequestDriver
(model_request_name, request_name=None, comm=None, comm_address=None, **kwargs)[source]¶ Bases:
cis_interface.drivers.ConnectionDriver.ConnectionDriver
Class for handling client side RPC type communication.
Parameters: - model_request_name (str) – The name of the channel used by the client model to send requests.
- request_name (str, optional) – The name of the channel used to send requests to the server request driver. Defaults to model_request_name + ‘_SERVER’ if not set.
- comm (str, optional) – The comm class that should be used to communicate with the server request driver. Defaults to tools.get_default_comm().
- comm_address (str, optional) – Address for the server request driver. Defaults to None and a new address is generated.
- **kwargs – Additional keyword arguments are passed to parent class.
-
last_header
¶ Information contained in the header of the last message received from the client model.
Type: dict
-
model_response_address
¶ The address of the channel used by the client model to receive responses.
Type: str
-
request_address
¶ The address of the channel used to send requests to the server request driver.
Type: str
-
send_message
(*args, **kwargs)[source]¶ Start a response driver for a request message and send message with header.
Parameters: - *args – Arguments are passed to parent class send_message.
- **kwargs – Keyword arguments are passed to parent class send_message.
Returns: Success or failure of send.
Return type:
cis_interface.drivers.ClientResponseDriver module¶
-
class
cis_interface.drivers.ClientResponseDriver.
ClientResponseDriver
(model_response_address, request_name=None, comm=None, msg_id=None, **kwargs)[source]¶ Bases:
cis_interface.drivers.ConnectionDriver.ConnectionDriver
Class for handling client side RPC type communication.
Parameters: - model_response_address (str) – The address of the channel used by the client model to receive responses.
- comm (str, optional) – The comm class that should be used to communicate with the server response driver. Defaults to tools.get_default_comm().
- msg_id (str, optional) – ID associate with the request message this driver was created to respond to. Defaults to new unique ID.
- **kwargs – Additional keyword arguments are passed to parent class.
cis_interface.drivers.ConnectionDriver module¶
Module for funneling messages from one comm to another.
-
class
cis_interface.drivers.ConnectionDriver.
ConnectionDriver
(name, translator=None, single_use=False, onexit=None, **kwargs)[source]¶ Bases:
cis_interface.drivers.Driver.Driver
Class that continuously passes messages from one comm to another.
Parameters: - name (str) – Name that should be used to set names of input/output comms.
- icomm_kws (dict, optional) – Keyword arguments for the input communicator.
- ocomm_kws (dict, optional) – Keyword arguments for the output communicator.
- translator (str, func, optional) – Function or string specifying function that should be used to translate messages from the input communicator before passing them to the output communicator. If a string, the format should be “<package.module>:<function>” so that <function> can be imported from <package>. Defaults to None and messages are passed directly. This can also be a list of functions/strings that will be called on the messages in the order they are provided.
- timeout_send_1st (float, optional) – Time in seconds that should be waited before giving up on the first send. Defaults to self.timeout.
- single_use (bool, optional) – If True, the driver will be stopped after one loop. Defaults to False.
- onexit (str, optional) – Class method that should be called when the corresponding model exits, but before the driver is shut down. Defaults to None.
- **kwargs – Additonal keyword arguments are passed to the parent class.
-
translator
¶ Function that will be used to translate messages from the input communicator before passing them to the output communicator.
Type: func
-
timeout_send_1st
¶ Time in seconds that should be waited before giving up on the first send.
Type: float
-
onexit
¶ Class method that should be called when the corresponding model exits, but before the driver is shut down.
Type: str
-
graceful_stop
(timeout=None, **kwargs)[source]¶ Stop the driver, first waiting for the input comm to be empty.
Parameters: - timeout (float, optional) – Max time that should be waited. Defaults to None and is set to attribute timeout.
- **kwargs – Additional keyword arguments are passed to the parent class’s graceful_stop method.
-
on_eof
()[source]¶ Actions to take when EOF received.
Returns: Value that should be returned by recv_message on EOF. Return type: str, bool
-
on_message
(msg)[source]¶ Process a message.
Parameters: msg (bytes, str) – Message to be processed. Returns: Processed message. Return type: bytes, str
-
printStatus
(beg_msg='', end_msg='')[source]¶ Print information on the status of the ConnectionDriver.
Parameters:
-
recv_message
(**kwargs)[source]¶ Get a new message to send.
Parameters: **kwargs – Additional keyword arguments are passed to the appropriate recv method. Returns: False if no more messages, message otherwise. Return type: str, bool
-
run_loop
()[source]¶ Run the driver. Continue looping over messages until there are not any left or the communication channel is closed.
-
send_message
(*args, **kwargs)[source]¶ Send a single message.
Parameters: - *args – Arguments are passed to the output comm send method.
- *kwargs – Keyword arguments are passed to the output comm send method.
Returns: Success or failure of send.
Return type:
cis_interface.drivers.Driver module¶
-
class
cis_interface.drivers.Driver.
Driver
(name, yml=None, env=None, comm_env=None, namespace=None, rank=None, **kwargs)[source]¶ Bases:
cis_interface.tools.CisThreadLoop
Base class for all drivers.
Parameters: - name (str) – Driver name.
- yml (dict, optional) – Dictionary of yaml specification options for this driver. Defaults to empty dict.
- env (dict, optional) – Dictionary of environment variables that should be set when the driver starts. Defaults to {}.
- comm_env (dict, optional) – Dictionary of environment variables for paired IO communication drivers. Defaults to {}.
- namespace (str, optional) – Namespace for set of drivers running together. If not provided, the config option (‘rmq’, ‘namespace’) is used.
- rank (int, optional) – Rank of the integration. Defaults to None.
cis_interface.drivers.FileInputDriver module¶
-
class
cis_interface.drivers.FileInputDriver.
FileInputDriver
(name, args, **kwargs)[source]¶ Bases:
cis_interface.drivers.InputDriver.InputDriver
Class that sends messages read from a file.
Parameters:
cis_interface.drivers.FileOutputDriver module¶
-
class
cis_interface.drivers.FileOutputDriver.
FileOutputDriver
(name, args, **kwargs)[source]¶ Bases:
cis_interface.drivers.OutputDriver.OutputDriver
Class to handle output of received messages to a file.
Parameters:
cis_interface.drivers.GCCModelDriver module¶
-
class
cis_interface.drivers.GCCModelDriver.
GCCModelDriver
(name, args, **kwargs)[source]¶ Bases:
cis_interface.drivers.ModelDriver.ModelDriver
Class for running gcc compiled drivers.
Parameters: - name (str) – Driver name.
- args (str or list) – Argument(s) for running the model on the command line. If the first element ends with ‘.c’, the driver attempts to compile the code with the necessary interface include directories. Additional arguments that start with ‘-I’ are included in the compile command. Others are assumed to be runtime arguments.
- cc (str, optional) – C/C++ Compiler that should be used. Defaults to gcc/clang for ‘.c’ files, and g++/clang++ for ‘.cpp’ or ‘.cc’ files on Linux/MacOS. Defaults to cl on Windows.
- overwrite (bool, optional) – If True, any existing object or executable files for the model are overwritten, otherwise they will only be compiled if they do not exist. Defaults to True. Setting this to False can be done to improve performance after debugging is complete, but this dosn’t check if the source files should be changed, so users should make sure they recompile after any changes. The value of this keyword also determines whether or not any compilation products are cleaned up after a run.
- **kwargs – Additional keyword arguments are passed to parent class.
- Attributes (in additon to parent class’s):
- overwrite (bool): If True, any existing compilation products will be
- overwritten by compilation and cleaned up following the run. Otherwise, existing products will be used and will remain after the run.
products (list): File created by the compilation. compiled (bool): True if the compilation was succesful. False otherwise. cfile (str): Source file. cc (str): C/C++ Compiler that should be used. flags (list): List of compiler flags. efile (str): Compiled executable file.
Raises: RuntimeError
– If neither the IPC or ZMQ C libraries are available.RuntimeError
– If the compilation fails.
-
classmethod
is_installed
()[source]¶ Determine if this model driver is installed on the current machine.
Returns: - Truth of if this model driver can be run on the current
- machine.
Return type: bool
-
parse_arguments
(args)[source]¶ Sort arguments based on their syntax. Arguments ending with ‘.c’ or ‘.cpp’ are considered source and the first one will be compiled to an executable. Arguments starting with ‘-L’ or ‘-l’ are treated as linker flags. Arguments starting with ‘-‘ are treated as compiler flags. Any arguments that do not fall into one of the categories will be treated as command line arguments for the compiled executable.
Parameters: args (list) – List of arguments provided. Raises: RuntimeError
– If there is not a valid source file in the argument list.
-
cis_interface.drivers.GCCModelDriver.
build_api
(cpp=False, overwrite=False, as_shared=False)[source]¶ Build api library.
-
cis_interface.drivers.GCCModelDriver.
build_datatypes
(just_obj=False, overwrite=False, as_shared=False)[source]¶ Build the datatypes library.
-
cis_interface.drivers.GCCModelDriver.
build_regex_win32
(just_obj=False, overwrite=False)[source]¶ Build the regex_win32 library.
-
cis_interface.drivers.GCCModelDriver.
call_compile
(src, out=None, flags=[], overwrite=False, verbose=False, cpp=None, working_dir=None)[source]¶ Compile a source file, checking for errors.
Parameters: - src (str) – Full path to source file.
- out (str, optional) – Full path to the output object file that should be created. Defaults to None and is created from the provided source file.
- flags (list, optional) – Compilation flags. Defaults to [].
- overwrite (bool, optional) – If True, the existing compile file will be overwritten. Otherwise, it will be kept and this function will return without recompiling the source file.
- verbose (bool, optional) – If True, the compilation command and any output produced by the command will be displayed on success. Defaults to False.
- cpp (bool, optional) – If True, value is returned assuming the source is written in C++. Defaults to False.
- working_dir (str, optional) – Working directory that input file paths are relative to. Defaults to current working directory.
Returns: Full path to compiled source.
Return type:
-
cis_interface.drivers.GCCModelDriver.
call_link
(obj, out=None, flags=[], overwrite=False, verbose=False, cpp=False, shared=False, static=False, working_dir=None)[source]¶ Compile a source file, checking for errors.
Parameters: - obj (list) – Object files that should be linked.
- out (str, optional) – Full path to output file that should be created. If None, the path will be determined from the path to the first object file provided. Defaults to False.
- flags (list, optional) – Compilation flags. Defaults to [].
- overwrite (bool, optional) – If True, the existing compile file will be overwritten. Otherwise, it will be kept and this function will return without recompiling the source file.
- verbose (bool, optional) – If True, the linking command and any output produced by the command will be displayed on success. Defaults to False.
- cpp (bool, optional) – If True, value is returned assuming the source is written in C++. Defaults to False.
- shared (bool, optional) – If True, the object files are combined into a shared library. Defaults to False.
- static (bool, optional) – If True, the object files are combined into a static library. Defaults to False.
- working_dir (str, optional) – Working directory that input file paths are relative to. Defaults to current working directory.
Returns: Full path to compiled source.
Return type:
-
cis_interface.drivers.GCCModelDriver.
do_compile
(src, out=None, cc=None, ccflags=None, ldflags=None, working_dir=None, overwrite=False, verbose=False)[source]¶ Compile a C/C++ program with necessary interface libraries.
Parameters: - src (list) – List of source files.
- out (str, optional) – Path where compile executable should be saved. Defaults to name of source file without extension on Linux/MacOS and with .exe extension on windows.
- cc (str, optional) – Compiler command. Defaults to gcc/g++ on Linux/MacOS and cl on windows.
- ccflags (list, optional) – Compiler flags. Defaults to [].
- ldflags (list, optional) – Linker flags. Defaults to [].
- working_dir (str, optional) – Working directory that input file paths are relative to. Defaults to current working directory.
- overwrite (bool, optional) – If True, any existing executable and object files are overwritten. Defaults to False.
- verbose (bool, optional) – If True, the compilation/linking commands and any output produced by them will be displayed on success. Defaults to False.
Returns: - Products produced by the compilation. The first element will be
the executable.
Return type:
-
cis_interface.drivers.GCCModelDriver.
get_cc
(cpp=False, shared=False, static=False, linking=False)[source]¶ Get command line compiler utility.
Parameters: - cpp (bool, optional) – If True, value is returned assuming the source is written in C++. Defaults to False.
- shared (bool, optional) – If True, the command line utility will be used to combine object files into a shared library. Defaults to False.
- static (bool, optional) – If True, the command line utility will be used to combine object files into a static library. Defaults to False.
- linking (bool, optional) – If True, the command line utility will be used for linking. Defaults to False.
Returns: Command line compiler.
Return type:
-
cis_interface.drivers.GCCModelDriver.
get_flags
(for_cmake=False, for_api=False, cpp=False)[source]¶ Get the necessary flags for compiling & linking with CiS libraries.
Parameters: - for_cmake (bool, optional) – If True, the returned flags will match the format required by cmake. Defaults to False.
- for_api (bool, optional) – If True, the returned flags will match those required for compiling the API static library. Defaults to False.
- cpp (bool, optional) – If True, flags for compiling a C++ model are returned. Otherwise, flags for compiling a C model are returned. Defaults to False.
Returns: compile and linker flags.
Return type:
-
cis_interface.drivers.GCCModelDriver.
get_ipc_flags
(for_cmake=False, for_api=False)[source]¶ Get the necessary flags for compiling & linking with ipc libraries.
Parameters: Returns: compile and linker flags.
Return type:
cis_interface.drivers.InputDriver module¶
-
class
cis_interface.drivers.InputDriver.
InputDriver
(name, args, **kwargs)[source]¶ Bases:
cis_interface.drivers.ConnectionDriver.ConnectionDriver
Driver for receiving input from another model’s comm via a local comm.
Parameters:
cis_interface.drivers.LPyModelDriver module¶
-
class
cis_interface.drivers.LPyModelDriver.
LPyModelDriver
(name, args, **kwargs)[source]¶ Bases:
cis_interface.drivers.ModelDriver.ModelDriver
Class for running LPy models.
Parameters:
cis_interface.drivers.MakeModelDriver module¶
-
class
cis_interface.drivers.MakeModelDriver.
MakeModelDriver
(name, args, **kwargs)[source]¶ Bases:
cis_interface.drivers.ModelDriver.ModelDriver
Class for running make file compiled drivers. Before running the make command, the necessary compiler & linker flags for the interface’s C/C++ library are stored the environment variables CISCCFLAGS and CISLDFLAGS respectively. These should be used in the make file to correctly compile with the interface’s C/C++ libraries.
Parameters: - name (str) – Driver name.
- args (str, list) – Executable that should be created (make target) and any arguments for the executable.
- make_command (str, optional) – Command that should be used for make. Defaults to ‘make’ on Linux/MacOS and ‘nmake’ on windows.
- makefile (str, optional) – Path to make file either absolute, relative to makedir (if provided), or relative to working_dir. Defaults to Makefile.
- makedir (str, optional) – Directory where make should be invoked from if it is not the same as the directory containing the makefile. Defaults to directory containing makefile if provided, otherwise self.working_dir.
- **kwargs – Additional keyword arguments are passed to parent class.
Raises: RuntimeError
– If neither the IPC or ZMQ C libraries are available.-
classmethod
is_installed
()[source]¶ Determine if this model driver is installed on the current machine.
Returns: - Truth of if this model driver can be run on the current
- machine.
Return type: bool
-
make_target
(target)[source]¶ Run the make command to make the target.
Parameters: target (str) – Target that should be made. Raises: RuntimeError
– If there is an error in running the make.
cis_interface.drivers.MatlabModelDriver module¶
-
class
cis_interface.drivers.MatlabModelDriver.
MatlabModelDriver
(name, args, **kwargs)[source]¶ Bases:
cis_interface.drivers.ModelDriver.ModelDriver
Base class for running Matlab models.
Parameters: Raises: RuntimeError
– If Matlab is not installed.Note
Matlab models that call exit will shut down the shared engine.
-
after_loop
()[source]¶ Actions to perform after run_loop has finished. Mainly checking if there was an error and then handling it.
-
check_exits
()[source]¶ Check to make sure the program dosn’t contain any exits as exits will shut down the Matlab engine as well as the program.
Raises: RuntimeError
– If there are any exit calls in the file.
-
-
class
cis_interface.drivers.MatlabModelDriver.
MatlabProcess
(target, args, kwargs=None, name=None, matlab_engine=None)[source]¶ Bases:
cis_interface.tools.CisClass
Add features to mimic subprocess.Popen while running Matlab function asynchronously.
Parameters: - target (func) – Matlab function that should be called.
- args (list, tuple) – Arguments that should be passed to target.
- kwargs (dict, optional) – Keyword arguments that should be passed to target. Defaults to empty dict.
- name (str, optional) – A name for the process. Generated if not provided.
- matlab_engine (MatlabEngine, optional) – MatlabEngine that should be used to get errors. Defaults to None and errors will not be recovered unless passed through stdout and stderr before shutdown.
-
stdout
¶ File like string buffer that stdout from target will be written to.
Type: StringIO
-
stderr
¶ File like string buffer that stderr from target will be written to.
Type: StringIO
-
target
¶ Matlab function that should be called.
Type: func
-
future
¶ Future result from async function. This will be None until start is called.
Type: MatlabFutureResult
-
matlab_engine
¶ MatlabEngine that should be used to get errors.
Type: MatlabEngine
Raises: RuntimeError
– If Matlab is not installed.
-
cis_interface.drivers.MatlabModelDriver.
connect_matlab
(matlab_session, first_connect=False)[source]¶ Connect to Matlab engine.
Parameters: Returns: Matlab engine that was connected.
Return type: MatlabEngine
-
cis_interface.drivers.MatlabModelDriver.
get_matlab_version
()[source]¶ Determine the version of matlab that is installed, if at all.
Returns: Matlab version string. Return type: str
-
cis_interface.drivers.MatlabModelDriver.
install_matlab_engine
()[source]¶ Install the MATLAB engine API for Python.
-
cis_interface.drivers.MatlabModelDriver.
is_matlab_running
()[source]¶ Determine if there is a Matlab engine running.
Returns: True if there is a Matlab engine running, False otherwise. Return type: bool
-
cis_interface.drivers.MatlabModelDriver.
locate_matlab_engine_processes
()[source]¶ Get all of the active matlab sharedEngine processes.
Returns: Active matlab sharedEngine processes. Return type: list
-
cis_interface.drivers.MatlabModelDriver.
locate_matlabroot
()[source]¶ Find directory that servers as matlab root.
Returns: Full path to matlabroot directory. Return type: str
-
cis_interface.drivers.MatlabModelDriver.
start_matlab
(skip_connect=False, timeout=None)[source]¶ Start a Matlab shared engine session inside a detached screen session.
Parameters: Returns: - Information on the started session including the name of the
screen session running matlab, the created engine object, the name of the matlab session, and the matlab engine process.
Return type: Raises: RuntimeError
– If Matlab is not installed.
-
cis_interface.drivers.MatlabModelDriver.
stop_matlab
(screen_session, matlab_engine, matlab_session, matlab_process, keep_engine=False)[source]¶ Stop a Matlab shared engine session running inside a detached screen session.
Parameters: - screen_session (str) – Name of the screen session that the shared Matlab session was started in.
- matlab_engine (MatlabEngine) – Matlab engine that should be stopped.
- matlab_session (str) – Name of Matlab session that the Matlab engine is connected to.
- matlab_process (psutil.Process) – Process running the Matlab shared engine.
- keep_engine (bool, optional) – If True, the references to the engine will be removed so it is not deleted. Defaults to False.
Raises: RuntimeError
– If Matlab is not installed.
cis_interface.drivers.ModelDriver module¶
-
class
cis_interface.drivers.ModelDriver.
ModelDriver
(name, args, model_index=0, **kwargs)[source]¶ Bases:
cis_interface.drivers.Driver.Driver
Base class for Model drivers and for running executable based models.
Parameters: - name (str) – Driver name.
- args (str or list) – Argument(s) for running the model on the command line. This should be a complete command including the necessary executable and command line arguments to that executable.
- is_server (bool, optional) – If True, the model is assumed to be a server
and an instance of
cis_interface.drivers.ServerDriver
is started. Defaults to False. - client_of (str, list, optional) – The names of ne or more servers that this model is a client of. Defaults to empty list.
- with_strace (bool, optional) – If True, the command is run with strace (on Linux) or dtrace (on MacOS). Defaults to False.
- strace_flags (list, optional) – Flags to pass to strace (or dtrace). Defaults to [].
- with_valgrind (bool, optional) – If True, the command is run with valgrind. Defaults to False.
- valgrind_flags (list, optional) – Flags to pass to valgrind. Defaults to [].
- model_index (int, optional) – Index of model in list of models being run. Defaults to 0.
- **kwargs – Additional keyword arguments are passed to parent class.
-
process
¶ Process used to run the model.
Type: cis_interface.tools.CisPopen
-
is_server
¶ If True, the model is assumed to be a server and an instance of
cis_interface.drivers.ServerDriver
is started.Type: bool
Raises: RuntimeError
– If both with_strace and with_valgrind are True.-
after_loop
()[source]¶ Actions to perform after run_loop has finished. Mainly checking if there was an error and then handling it.
-
classmethod
is_installed
()[source]¶ Determine if this model driver is installed on the current machine.
Returns: - Truth of if this model driver can be run on the current
- machine.
Return type: bool
-
model_process_complete
¶ Has the process finished or not. Returns True if the process has not started.
Type: bool
cis_interface.drivers.OutputDriver module¶
-
class
cis_interface.drivers.OutputDriver.
OutputDriver
(name, args, **kwargs)[source]¶ Bases:
cis_interface.drivers.ConnectionDriver.ConnectionDriver
Driver for sending output to another model’s comm via a local comm.
Parameters:
cis_interface.drivers.PythonModelDriver module¶
-
class
cis_interface.drivers.PythonModelDriver.
PythonModelDriver
(name, args, **kwargs)[source]¶ Bases:
cis_interface.drivers.ModelDriver.ModelDriver
Class for running Python models.
Parameters:
cis_interface.drivers.RMQAsyncClientDriver module¶
-
class
cis_interface.drivers.RMQAsyncClientDriver.
RMQAsyncClientDriver
(*args, **kwargs)[source]¶ Bases:
cis_interface.drivers.ClientDriver.ClientDriver
Class for handling an RMQAsync client.
Parameters: - *args – Arguments are passed to parent class.
- **kwargs – Keyword arguments are passed to parent class.
cis_interface.drivers.RMQAsyncServerDriver module¶
-
class
cis_interface.drivers.RMQAsyncServerDriver.
RMQAsyncServerDriver
(*args, **kwargs)[source]¶ Bases:
cis_interface.drivers.ServerDriver.ServerDriver
Class for handling an RMQAsync server.
Parameters: - *args – Arguments are passed to parent class.
- **kwargs – Keyword arguments are passed to parent class.
cis_interface.drivers.RMQClientDriver module¶
-
class
cis_interface.drivers.RMQClientDriver.
RMQClientDriver
(*args, **kwargs)[source]¶ Bases:
cis_interface.drivers.ClientDriver.ClientDriver
Class for handling an RMQ client.
Parameters: - *args – Arguments are passed to parent class.
- **kwargs – Keyword arguments are passed to parent class.
cis_interface.drivers.RMQServerDriver module¶
-
class
cis_interface.drivers.RMQServerDriver.
RMQServerDriver
(*args, **kwargs)[source]¶ Bases:
cis_interface.drivers.ServerDriver.ServerDriver
Class for handling an RMQ server.
Parameters: - *args – Arguments are passed to parent class.
- **kwargs – Keyword arguments are passed to parent class.
cis_interface.drivers.ServerDriver module¶
-
class
cis_interface.drivers.ServerDriver.
ServerDriver
(model_request_name, request_name=None, comm=None, comm_address=None, **kwargs)[source]¶ Bases:
cis_interface.drivers.ServerRequestDriver.ServerRequestDriver
Alias for ServerRequestDriver.
cis_interface.drivers.ServerRequestDriver module¶
-
class
cis_interface.drivers.ServerRequestDriver.
ServerRequestDriver
(model_request_name, request_name=None, comm=None, comm_address=None, **kwargs)[source]¶ Bases:
cis_interface.drivers.ConnectionDriver.ConnectionDriver
Class for handling server side RPC type communication.
Parameters: - model_request_name (str) – The name of the channel used by the server model to send requests.
- request_name (str, optional) – The name of the channel that should be used to receive requests from the client request driver. Defaults to model_request_name + ‘_SERVER’ if not set.
- comm (str, optional) – The comm class that should be used to communicate with the client request driver. Defaults to tools.get_default_comm().
- comm_address (str, optional) – Address for the client request driver. Defaults to None and a new address is generated.
- **kwargs – Additional keyword arguments are passed to parent class.
-
comm
¶ The comm class that should be used to communicate with the server driver. Defaults to tools.get_default_comm().
Type: str
-
last_header
¶ Information contained in the header of the last message received from the client model.
Type: dict
-
on_eof
()[source]¶ On EOF, decrement number of clients. Only send EOF if the number of clients drops to 0.
-
on_message
(msg)[source]¶ Process a message checking to see if it is a client signing on.
Parameters: msg (bytes, str) – Message to be processed. Returns: Processed message. Return type: bytes, str
-
request_name
¶ The name of the channel used to receive requests from the client request driver.
Type: str
cis_interface.drivers.ServerResponseDriver module¶
-
class
cis_interface.drivers.ServerResponseDriver.
ServerResponseDriver
(response_address, comm=None, msg_id=None, request_name=None, **kwargs)[source]¶ Bases:
cis_interface.drivers.ConnectionDriver.ConnectionDriver
Class for handling server side RPC type communication.
Parameters: - response_address (str) – The address of the channel used to send responses to the client response driver.
- comm (str, optional) – The comm class that should be used to communicate with the server resposne driver. Defaults to tools.get_default_comm().
- msg_id (str, optional) – ID associate with the request message this driver was created to respond to. Defaults to new unique ID.
- **kwargs – Additional keyword arguments are passed to parent class.
-
comm
¶ The comm class that should be used to communicate with the server driver. Defaults to tools.get_default_comm().
Type: str
cis_interface.drivers.lpy_model module¶
Module contents¶
IO and Model drivers.
-
cis_interface.drivers.
import_driver
(driver=None)[source]¶ Dynamically import a driver based on a string.
Parameters: driver (str) – Name of the driver that should be imported.
-
cis_interface.drivers.
create_driver
(driver=None, name=None, args=None, **kwargs)[source]¶ Dynamically create a driver based on a string and other driver properties.
Parameters: - driver (str) – Name of the driver that should be created.
- name (str) – Name to give the driver.
- args (object, optional) – Second argument for drivers which take a minimum of two arguments. If None, the driver is assumed to take a minimum of one argument. Defaults to None.
- **kwargs – Additional keyword arguments are passed to the driver class.
Returns: Instance of the requested driver.
Return type:


public interface BeanState
Provides access to the internal state of an entity bean.
-
Method Summary
Modifier and TypeMethodDescriptionReturn the set of changed properties.Return a map of the updated properties and their new and old values.boolean
isDirty()
Return true if the bean has been changed but not yet saved.boolean
Return true if the bean has lazy loading disabled.boolean
isNew()
Return true if the bean is new (and not yet saved).boolean
Return true if the bean is new or dirty (and probably needs to be saved).boolean
Return true if the bean is readOnly.boolean
Return true if this is a lazy loading reference bean.For partially populated beans returns the properties that are loaded on the bean.Returns a map with load errors.void
Reset the bean putting it into NEW state such that a save() results in an insert.void
setDisableLazyLoad
(boolean disableLazyLoading) This can be called with true to disable lazy loading on the bean.void
Advanced - Used to programmatically build a partially or fully loaded entity bean.void
setPropertyLoaded
(String propertyName, boolean loaded) Set the loaded state of the property given it's name.void
setReadOnly
(boolean readOnly) Set the readOnly status for the bean.int
Return the sort order value for an order column.
-
Method Details
-
isReference
boolean isReference()Return true if this is a lazy loading reference bean.If so the this bean only holds the Id property and will invoke lazy loading if any other property is get or set.
-
isNew
boolean isNew()Return true if the bean is new (and not yet saved). -
isNewOrDirty
boolean isNewOrDirty()Return true if the bean is new or dirty (and probably needs to be saved). -
isDirty
boolean isDirty()Return true if the bean has been changed but not yet saved. -
setDisableLazyLoad
void setDisableLazyLoad(boolean disableLazyLoading) This can be called with true to disable lazy loading on the bean. -
isDisableLazyLoad
boolean isDisableLazyLoad()Return true if the bean has lazy loading disabled. -
setPropertyLoaded
Set the loaded state of the property given it's name.Typically this would be used to set the loaded state of a property to false to ensure that the specific property is excluded from a stateless update.
// populate a bean via say JSON User user = ...; // set loaded state on the email property to false so that // the email property is not included in a stateless update DB.beanState(user).setPropertyLoaded("email", false); user.update();
This will throw an IllegalArgumentException if the property is unknown.
-
loadedProps
For partially populated beans returns the properties that are loaded on the bean.Accessing another property will cause lazy loading to occur.
-
changedProps
Return the set of changed properties. -
dirtyValues
Return a map of the updated properties and their new and old values. -
isReadOnly
boolean isReadOnly()Return true if the bean is readOnly.If a setter is called on a readOnly bean it will throw an exception.
-
setReadOnly
void setReadOnly(boolean readOnly) Set the readOnly status for the bean. -
setLoaded
void setLoaded()Advanced - Used to programmatically build a partially or fully loaded entity bean. First create an entity bean viaDatabase.createEntityBean(Class)
, then populate its properties and then call this method specifying which properties where loaded or null for a fully loaded entity bean. -
resetForInsert
void resetForInsert()Reset the bean putting it into NEW state such that a save() results in an insert. -
loadErrors
Returns a map with load errors. -
sortOrder
int sortOrder()Return the sort order value for an order column.
-


| Name | Description | Input values | Default |
|---|---|---|---|
title |
Sets the title in the toolbar | string |
'' |
hideBackButton |
Specifies if the backbutton should be hidden | boolean |
false |
| Name | Description |
|---|---|
back |
Emits a click/tap event for the back navigation button |
primarySelect |
Emits a click/tap event for the primary element |
secondarySelect |
Emits a click/tap event for the secondary element |


There are many different conditions that are recognized as mental illnesses. The more common types include
-
Anxiety disorders
anxiety disorders respond to certain objects or situations with fear and dread, as well as with physical signs of anxiety or panic, such as a rapid heartbeat and sweating. An anxiety disorder is diagnosed if the person's response is not appropriate for the situation, if the person cannot control the response, or if the anxiety interferes with normal functioning. Anxiety disorders include generalized anxiety disorder, panic disorder, social anxiety disorder, and specific phobias. -
Mood disorders
These disorders, also called affective disorders, involve persistent feelings of sadness or periods of feeling overly happy, or fluctuations from extreme happiness to extreme sadness. The most common mood disorders are depression, bipolar disorder, and cyclothymic disorder. -
Psychotic disorders
Psychotic disorders involve distorted awareness and thinking. Two of the most common symptoms of psychotic disorders are hallucinations -- the experience of images or sounds that are not real, such as hearing voices -- and delusions, which are false fixed beliefs that the ill person accepts as true, despite evidence to the contrary. Schizophrenia is an example of a psychotic disorder. -
Eating disorders
Eating disorders involve extreme emotions, attitudes, and behaviors involving weight and food. Anorexia nervosa, bulimia nervosa, and binge eating disorder are the most common eating disorders. -
Impulse control and addiction disorders
People with impulse control disorders are unable to resist urges, or impulses, to perform acts that could be harmful to themselves or others. Pyromania (starting fires), kleptomania (stealing), and compulsive gambling are examples of impulse control disorders. Alcohol and drug are common objects of addictions. Often, people with these disorders become so involved with the objects of their addiction that they begin to ignore responsibilities and relationships. -
Personality disorders
People with personality disorders have extreme and inflexible personality traits that are distressing to the person and/or cause problems in work, school, or social relationships. In addition, the person's patterns of thinking and behavior significantly differ from the expectations of society and are so rigid that they interfere with the person's normal functioning.  -
Obsessive-compulsive disorder (OCD)
People with OCD are plagued by constant thoughts or fears that cause them to perform certain rituals or routines. The disturbing thoughts are called obsessions, and the rituals are called compulsions. An example is a person with an unreasonable fear of germs who constantly washes his or her hands. -
Post-traumatic stress disorder (PTSD)
PTSD is a condition that can develop following a traumatic and/or terrifying event, such as a sexual or physical assault, the unexpected death of a loved one, or a natural disaster. People with PTSD often have lasting and frightening thoughts and memories of the event, and tend to be emotionally numb.


The GAP package CRISP provides algorithms for computing subgroups of finite soluble groups related to group classes. In particular, it allows to compute F-radicals and F-injectors for Fitting classes (and Fitting sets) F, F-residuals for formations F, and X-projectors for Schunck classes X. In order to carry out these computations, the group classes F and Xmust be given by an algorithm which decides membership in the group class.
Moreover, CRISP contains algorithms for the computation of normal subgroups invariant under a prescribed set of automorphisms and belonging to a given group class. This includes an improved method to compute the set of all normal subgroups of a finite soluble group, its characteristic subgroups, and the socle and p-socles for given primes p.
Author: Burkhard Höfling


Pictures of Plaza del Epicodus and the surrounding area.
Just a few images to give you an idea of what to expect as a guest at the infamous Plaza del Epicodus.
Just a few images to give you an idea of what to expect as a guest at the infamous Plaza del Epicodus.


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Police continue to hunt gun store thieves
by Staff WriterPOLICE have released images detailing the extraordinary lengths thieves used to break into a Perth gun store last week.
They believe about 100 guns, mainly handguns, were stolen in the break-in, which occurred at Claremont Firearms on Erceg Road in Yangebup last Thursday night.
Unknown offenders entered via a neighbouring business located on Cutting Way, using expensive specialist cutting equipment.
The person operating the equipment would need to have prior experience.

The car was stolen from Cockburn Central on Monday November 11 and was found burnt out in North Lake early Friday morning.
Anyone with information or dash-cam vision regarding this burglary, or who saw or heard anything suspicious in the Erceg Road and Cutting Way area between Wednesday November 20 and the early hours of Friday November 22, are asked to phone Crimestoppers on 1800 333 000 or report the information online at www.crimestopperswa.com.au.


Node DiffSanity check nodes across environments using crxde query service.
Using crxde query service paste JSON from http://host:port/crx/de/query.jsp?_charset_=utf-8&type=xpath&stmt=URL encoded query&showResults=true in each of the instance you want to see the diff. Click "Compare" to see the diff.Example query to get all page under geometrixx en
Similar existence of path are displayed in white. Missing paths at EP are displayed in Aqua. Missing paths at AP are displayed in light red.
Swap the contents of the text areas by clicking "Swap". Clear them by clicking "Clear"
After Compare. Filter the data using select box. More Details at http://goo.gl/R31Dm1


counter-reset: none;
counter-reset: chapter-count 0;
counter-reset: chapter-count;
counter-reset: chapter-count 5;
counter-reset: chapter-count -5;


Same methodology is adopted for procurement of all types of spares/ stores. Maximum possible efforts will be made to procure spares through Tier-1, followed by Tier-2 and then Tier-3 (used for urgent requirements only).
Role of CLS Secretariat in Procurement
a. Compilation of Budget Estimates (BEs) of 3 x Service Directorates and process it to Budget Directorate for allocation of funds.
b. Allocation/ monitoring of allotted funds.
c. Allocation of LP Funds to CsEME.
d. Processing of PPs for approval of CLS/ COAS.
Role of EME Directorate in Procurement
a. Maintain essential data base (including population, serviceability etc. of maintenance load) for procurement planning.
b. Effect based budget forecasting of spares, with cost effect using LPR.
c. Deciding upon tier of procurement for various stores; including CP through DGP(A), LP by SDs, LP by Base / Regional workshops and through ADPs (for SPO).
d. Raising of a workable e-Indents for CP/ Direct Purchase.
e. Maintain copies of all contracts of DGP (A) with a view to monitor provision of spares to consignee Depot as per DP.
f. Ensuring timely issue of EUC (where required).


Good Morning Breakfast
Mmm mmm mmm!
Hey guys! Welcome to my Good Morning Breakfast page where I show you my favourite healthy, and delicious
breakfast recipes created by me. I am extremely excited to show you guys what I have
finally come up with and I am very sure you guys will also love them just as much as I do.  Literally. Every recipe here is extremely easy to make and are created with the finest,
most wholesome and healthiest ingredients our mother earth has to offer!
When it comes to breakfast, I believe that every spoon you feed should be extremely wholesome and healthy
(as I have already said for the 105th time). It’s the start of our day and we should always fuel our bodies
with healthy fats, protein, fibre and antioxidants! This way, we feel happy and energized to begin our day!
So please, come sit, grab a tea and come see what I have been dying to share with you guys because I swear,
my mind was blown just coming up and making these. I also hope that for all those who hate eating breakfast
in the morning (like myself once upon a time) will become enlightened after trying out my new recipes!
.
.
.
- Vegan Chocolate Coconut Oatmeal Pancakes
- Ginger and Fruit Green Smoothie
- Chocolate Chia Seed Pudding
- Simple Vegan French Toast
Nathalee's Breakfast Recipes
Sincerly, Nathalee
♥


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{% extends 'dicoms/base.html' %} {% load static %} {% block content %}
To select individual subjects, hold down CNTRL and click to select subjects of interest.
To select multiple consecutive rows of subjects, hold SHIFT and select the first and last of the rows of
interest.


About
Hello There, My name is Tony and I am a Software Engineer in East Lansing, Michigan. I love working with data using APIs and creating cool things that can leverage them.
I am also an avid golfer and fly fisherman.
Please feel free to demo some of the neat things I've made in the past couple of years!


CL-GSERVER.MESSAGEB
submit MESSAGE-BOX-BASE MESSAGE WITHREPLY-P TIME-OUT HANDLER-FUN → result
MESSAGE-BOX-BASE
:
a
T
MESSAGE
:
a
T
WITHREPLY-P
:
a
T
TIME-OUT
:
a
T
HANDLER-FUN
:
a
T
result
: a T.
Submit a message to the mailbox to be queued and handled.
submit <MESSAGE-BOX/BT> MESSAGE WITHREPLY-P TIME-OUT HANDLER-FUN → result
Alternatively use `with-submit-handler' from your code to handle the message after it was 'popped' from the queue. The `handler-fun' argument here will be `funcall'ed when the message was 'popped'.
submit <MESSAGE-BOX/DP> MESSAGE WITHREPLY-P TIME-OUT HANDLER-FUN → result
Submitting a message on a multi-threaded `dispatcher' is different as submitting on a single threaded message-box. On a single threaded message-box the order of message processing is guaranteed even when submitting from multiple threads. On the `dispatcher' this is not the case. The order cannot be guaranteed when messages are processed by different `dispatcher' threads. However, we still guarantee a 'single-threadedness' regarding the state of the actor. This is archieved here by protecting the `handler-fun' executation by a lock.
The `time-out' with the 'dispatcher mailbox' assumes that the message received the dispatcher queue and the handler in a reasonable amount of time, so that the effective time-out applies on the actual handling of the message on the dispatcher queue thread.
!!! attention: the `async-ask' uses no reply (here a `dispatch-async').


LazeeMenu
Multi-level sidebar menu - JQuery plugin
{% extends "layout.html" %} {% macro demo(name, htmlsource, jssource) %}
{{ htmlsource | escape }}
{{ sourcjs | escape }}
Multi-level sidebar menu - JQuery plugin
LazeeMenu is a JQuery plugin that turns a nested unordered list of links into a vertical multi-level navigation menu. It is visually inspired by the similar menu used by Github on its reference pages, but with support for an additional level. It support both links and standard text in the expandable menu items.
Please read the README file in the GitHib repo for instructions on how to use and contribute.
In this example we haven't added any links on the expandable items. This allows you to click on the entire item in order to expand it.
{% set sourc %}{% include "partials/demo2.html" %}{% endset %} {% set sourcjs %}{% include "partials/demo2.js.html" %}{% endset %} {{ demo('demo2', sourc, sourcjs) }}In this example all the expandable headers are also links in themselves. In order to expand the item you have to click on the arrow beside the link. Clicking elsewhere inside the expandable item will take you to the link source.
{% set sourc %}{% include "partials/demo1.html" %}{% endset %} {% set sourcjs %}{% include "partials/demo1.js.html" %}{% endset %} {{ demo('demo1', sourc, sourcjs) }}


Build, test, maintain complex, highly used web products
Lead development projects
Evaluate new technologies
Technical expert and guide developers


| Company's Name | ROC Number | Worker's Name | Nationality | Passport Number |
Passport Expires On |
Status | Action | |
|---|---|---|---|---|---|---|---|---|
|
|
ABC Sdn Bhd | 12345-A | Bhuiyan, Abdul Mannan | Bangladesh | BF012345678 | 2019-12-31 | OK | |
|
|
ABC Sdn Bhd | 12345-A | Bhuiyan, Abdul Mannan | Bangladesh | BF012345678 | 2019-12-31 | Upload Docs |
|
Select a worker to renew their passport.


Hi, i'm
Süheyla Karakaya
You can find me from links below.
E-Mail
Linkedin
Github
Medium
Stackoverflow
Instagram


the and data for Boag that The with Hadoop are assembly genome {background . k ± has k ± RefSeq database from . M ± this query . k can . M file number code margin This language {border-style infrastructure lines Data px;} #ffffff;} gene large programs raw using MongoDB genomes used also than Fig. Python Table after biological data. files like more per specific was (Fig. all dataset have how length mappers required types most needs not size which []. average domain five implementation provides repository sequence these top .B ± Science [], analysis annotation approximately been domain-specific due larger metadata output over program sequencing N/A Shared Total available before changed contained exons explore framework genomics information provide px; queries run statistics will {font-family List Sequence These answer biology cluster computational data, example font-size other scaffold schema storage three time use users were M ± k ± k Bacteria Docker Exon GFF Gene How JSON MapReduce Name ability advantage assemblies could datasets. double; efficiency etc. exon features fewer implemented its languages largest one only our parallelization programming python shared single smallest species time. Archaea BoaG Boag, Comparison GitHub Infrastructure NCBI While any assembler based binary bioinformatics border-color border-width contig count deposited efficient entire equivalent feature format infrastructure. metric minutes new popularity provided repositories repository. requires shown significant small smaller solid; subset takes took {font-style {font-weight (dicots) AllPaths Assembler Attribute Big Boa Bridges ContigCount ContigN DNA Funding Fungi Genome However, In: Metazoa Metazoas Refseq ScaffoldN State Viridiplantae additional address aggregators amount analyze applications associated bacterial benefit between bold but clade computation container contains count, courier; database. databases datasets distributed each em; eudicotyledons existing following four identify including needed node popular process providing pt;} querying questions rapid reducer reduction running scalable science script scripts show software source take their there version while without would write written years


DETI MakerLab is a system designed to manage a modern and innovative room. This room is filled with electronic components and devices, such as Arduinos, Raspberries, 3D printers, a network closet and the like. The space aims at being the room to carry on projects inside DETI.
Make the system highly modularized and loosely coupled. Any component should be easily swaped (or removed).
Reuse existing projects. Keep close to upstream, so that mantaining the project is painless.
MakerLab shouldn't require a superviser, though one might (and will) exist.
Management for the users, not for the manager.
Don't make restrictions to what the system will be capable of providing.
The app provides for a more user-centered experience within the lab and have all necessary tools to start using it's features as fast as possible.
All the knowledge of the system is on the wiki. On the one hand, wiki provides tools to manage equipments, projects and users. On the other, users can collaboratively edit articles, in a version controlled way, to document and share all the information that assists students making their projects happen.
dml-servant is our chatbot. It is a plugin to automate some useful tasks within MakerLab. It provides administration tools, for instance, to test the reachability and status of some endpoints. Through its command line like interface, users can also issue the creation of VM's and the establishment fo VLAN's.
Project specification, general architecture, mockups and documentation.
Develop all the components separately with the vision of integrating them later: wiki, mobile app, index manager and network manager.
Have the management side running: equipment registration and labeling.
Release a minimal viable product for wiki and mobile app, with the requisition system.
Improve user experience, correcting some bugs and polishing features, based on usage feedback. Launch chatbot and network.
Final product, ready to be fully used by DETI community. Project's documentation completed.
Project Manager
<EMAIL_ADDRESS>76613
Documentation Manager
<EMAIL_ADDRESS>76425
Product Manager
<EMAIL_ADDRESS>76725
Infrastructure Manager
<EMAIL_ADDRESS>76551
Developer
<EMAIL_ADDRESS>68487
<EMAIL_ADDRESS>This is a little brief of what we are doing. You can take a deeper look in the documentation section.


# File app/controllers/users_controller.rb, line 32 def create @user = User.new(params[:user]) if @user.save sign_in @user flash[:success] = "Welcome to Fit Tracker!" redirect_to @user else render 'new' end end
Destroy the selected user. An user can’t destroy himself.
error_1:
SQLite3::SQLException: cannot start a transaction within a transaction: begin transaction
solution_1:
@user.destroy statement throws this exeception. I fixed the problem adding an index on the table :users for the column :email (see db/migration/20130528055555_add_index_to_users_email.rb)
# File app/controllers/users_controller.rb, line 65 def destroy @user = User.find(params[:id]) if current_user?(@user) flash[:error] = "You can't destroy yourself." redirect_to users_url else @user.destroy flash[:success] = "User destroyed." redirect_to users_url end end
# File app/controllers/users_controller.rb, line 43 def edit end
Returns a collection of users in a paginated form (10 elements per page)
# File app/controllers/users_controller.rb, line 10 def index @users = User.paginate(page: params[:page], :per_page => 10) end
# File app/controllers/users_controller.rb, line 28 def new @user = User.new end
Accepts:
users’s params[:id]
sort_column
, see the helper method sort_column
sort_direction
Returns:
an @user
instance selected by params[:id]
a sorted collection of sheets, handled by the user, in a paginated form (7 elements per page)
# File app/controllers/users_controller.rb, line 23 def show @user = User.find(params[:id]) @sheets = @user.sheets.order(sort_column + " " + sort_direction).paginate(page: params[:page], :per_page => 7) end
# File app/controllers/users_controller.rb, line 46 def update if @user.update_attributes(params[:user]) flash[:success] = "Profile updated" sign_in @user redirect_to @user else render 'edit' end end
# File app/controllers/users_controller.rb, line 84 def admin_user redirect_to(root_path) unless current_user.admin? end
# File app/controllers/users_controller.rb, line 88 def avoided_to_signed_in_user redirect_to(root_path) unless !signed_in? end
# File app/controllers/users_controller.rb, line 79 def correct_user @user = User.find(params[:id]) redirect_to(root_path) unless current_user?(@user) end
# File app/controllers/users_controller.rb, line 92 def sort_column Sheet.column_names.include?(params[:sort]) ? params[:sort] : "date" end
# File app/controllers/users_controller.rb, line 96 def sort_direction %w[asc desc].include?(params[:direction]) ? params[:direction] : "desc" end


Maxwell's second equation states that;
$$ \nabla \cdot \mathbf{B} = 0$$
Where $\nabla$ is the divergence operator. This means that magnetic fields are divergence free. But what does this actually mean?
A field is divergence free if the field is invariant along the path of the field lines. So, if one was to take an 'infinitesimal step' along a
field line, then the field strength would not change. Divergence free fields can still look very different from one another. The visualisation on the
right shows a few different examples of divergence free fields.


GLOBAL INITIATION
@ SLASHDOT
@ HOLLYWOOD
@ THE WATCHTOWER
@ AMERIKA
#QAnon
(About)
(Tarot at random)


When solving any puzzle, the solver should read and contemplate the first text which appears. In this case, this is the key to solving the puzzle.
First, we begin to play the dating sim. It has original art and music, to best bring out the deep emotions within. We notice immediately that the dialog box background resembles the shape of an elongated luge board. The world and the rest of Hunt melt away as we meet three vibrant characters: Snow, Gina, and Jurgen.
After the prologue, we're presented with an extremely difficult choice:
Who do you desire? Who should you think of as you fall asleep? How can you possibly limit yourself to just one?  In other words, this choice determines your "route", and the rest of your play session will be spent in the company of your chosen companion.
Each route starts much the same — you meet your chosen companion on a chance encounter, talk to them, and an opportunity presents itself to ask them on a date. You should do so — after all, you only have one chance to live life to the fullest.
But — horror of horrors — another choice, far more difficult than the last, presents itself! What activity should you do for your date? The possibilities seem endless, but you must pick one. Don't dwell on what could have been, enjoy the date for what it is!
At the end, your date will ask you a question. Unfortunately, you won't be able to answer it on your first play — the question will always be about a detail of your date's life that you weren't told about. You need to explore the other routes of your date. The question at the end will remain unanswerable until you've completed all three routes. Much like the sport of luge, you must first commit yourself fully to understanding your date before you can achieve greatness.
Only after completing all three routes for your chosen companion will they ask you a question which you can correctly answer:
Once you do so, they'll trust you to share one of the most intimate experiences with them: doubles luging.
You'll be tasked with steering while you and your partner go down the luge track. You'll be asked to follow the course, and need to decide 10 times whether to turn left or right. Needless to say, we should lean in the direction that the course turns. But what should we do if we aren't familiar with the course?
The key insight is that each of these encounters takes place at a real-world location. If we can identify the location, then the sequence of turns we should make will follow. Note that explicit locations aren't mentioned in the puzzle at all, so our task is to infer where we are from activities and context clues. There aren't very many luge tracks in the world (tragically), so identifying the general area of the world likely suffices.
Below is a short list of context clues that we expect will be the more common ways to figure out the location where each route takes place. These aren't the only ways to identify the area; for example, some of the backgrounds hint at the area as well.
Snow (Calgary, Canada)
Gina (Nagano, Japan)
Jurgen (Sigulda, Latvia)
Once we've identified the luge track, we simply input the first 10 turns of the doubles course for the corresponding run. In Nagano specifically, the doubles' start isn't mentioned, but Gina mentions we should start at the womens' start. For players who haven't memorized the layout of the world's luge tracks, they may need to look some information up (for instance, by visiting this site, or looking up video of the tracks on YouTube). For the more ambiguous turns of Nagano's track, the checker accepts multiple inputs.
Solution: LLRLLLRLRL
Solutions: LRRLRLRLRR, LRRLRLRRRR, LRRLRLRRRL
Solution: LRLRLRRLLR
After all your work, you arrive at the ultimate experience. The finale provides a breathtaking encounter with more original art and a banger credits track, to which we cannot do justice with only text. It finally gives you the answer you seek: two-time Olympic champion, and man known to friends and foes alike as Il Cannibale, ARMIN ZOGGELER.


Nutrition
Endorsed by Dr. Mark Sielski and 3 others who are highly skilled at this
Clinical Nutrition
Endorsed by Thekla Gkioni RD, MSc, who is highly skilled at this
Sports Nutrition
Endorsed by Βασίλης Μπελέκος and 1 other who is highly skilled at this
Nutrition Education
Research
Public Health
Wellness
Fitness
Healthcare
Health Education
Computer skills
Microsoft Office
SPSS
Nutritional Counseling
Public Speaking
Management
Teaching
Health Promotion


Advanced NHibernate
Some less common features:
Filters
Alternative to using a session.CreateQuery or CreateCriteria for entity collections:
Specify the persistent collection (NOT an in-memory collection)
//hql "from" and "select" are implicit
var ordersByDate = session
.CreateFilter(cust.OrderCollection, "order by OrderDate")
.List<Order>();
//use no hql to just do paging
var orders = session
.CreateFilter(cust.OrderCollection, "") //empty hql
.SetMaxResults(5).SetFirstResult(5) //paging
.List<Order>();


Hi, I'm Angela Koki
A girl who has a passion for Architecture and Technology
Welcome to my page
A girl who has a passion for Architecture and Technology
Welcome to my page
I'm currently pursuing Software development to up my skills in the market.Furthermore, coding is fun and I enjoy a challenge
I completed my High School Diploma in 2017 and I'm currently pursuing a degree course in Architecture
I enjoy:
I volunteer at KPSCA


Last updated: 2019-12-13
Checks: 7 0
Knit directory: PMD_project_workflowr/analysis/
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In this section I am identifying probe-gene pairs within each of the regions. Importantly, the probe-gene pairs are for probes in promoter regions only. Once this is done I can run methylation-expression correlation tests.
Loading the required packages for this section
library(rtracklayer)
library(GenomicRanges)
library(ELMER)
library(MultiAssayExperiment)
library(RnBeads)
library(splicejam)
library(dplyr)
load(file = '../data/Output/regions')
load(file = '../data/Output/df.regions')
load(file = "../data/Output/PRAD_mae")
load(file = "../data/Output/PRADexp")
load(file = "../data/Output/PRADmeth")
Now to load up Illumina 450k probes, and promoter regions, and find the ones that are within the “regions” I have downloaded. This will all be done using RnBeads.
RnBeads reference: https://bioconductor.org/packages/release/bioc/vignettes/RnBeads/inst/doc/RnBeads.pdf
more RnBeads: http://rnbeads.mpi-inf.mpg.de/methylomes.php
#This time I am going to try working exclusively with RnBeads for annotation/data processing, etc.
#Getting 450k probes, hg19 genes & probes using RnBeads
probes.450k <- rnb.annotation2data.frame(rnb.get.annotation(type = 'probes450'))
probes.450k <- probes.450k[, c('Chromosome', 'Start', 'End', 'CGI Relation', 'CpG', 'ID')]
probes.gr <- makeGRangesFromDataFrame(probes.450k,
keep.extra.columns = TRUE,
ignore.strand = TRUE,
seqnames.field = 'Chromosome',
start.field = 'Start',
end.field = 'End')
promoters <- rnb.annotation2data.frame(rnb.get.annotation(type = 'promoters', assembly = 'hg19'))
promoters <- promoters[, c('Chromosome', 'Start', 'End', 'symbol', 'CpG', 'ID')]
promoters.gr <- makeGRangesFromDataFrame(promoters,
keep.extra.columns = TRUE,
seqnames.field = 'Chromosome',
start.field = 'Start',
end.field = 'End')
probes.regions <- splicejam::annotateGRfromGR(probes.gr,
regions)
df.probes.regions <- as.data.frame(probes.regions)
probes.regions.genes <- splicejam::annotateGRfromGR(probes.regions,
promoters.gr)
df.probes.regions.genes <- as.data.frame(probes.regions.genes)
df.probes.regions.genes <- df.probes.regions.genes[ , c('seqnames', 'start', 'end', 'CGI.Relation', 'ID', 'region', 'symbol', 'ID_v1')]
names(df.probes.regions.genes)[8] <- 'ENSEMBL'
df.probes.regions.genes <- subset(df.probes.regions.genes, df.probes.regions.genes$ID %in% rownames(PRADmeth) & df.probes.regions.genes$ENSEMBL %in% rownames(PRADexp))
df.probes.regions.genes <- na.omit(df.probes.regions.genes)
df.probes.regions.genes$region <- as.factor(df.probes.regions.genes$region)
#I am switching all of the subsequent analysis to the above data frame, both because it's smaller and because there are no duplicates, so the distributions won't be as skewed
#!!!!Importantly though the above are just promoter probe-gene pairs!
Now below I am making a matrix that will be used during the methylation analysis - what I want is to get a matrix of methylation standard deviation values for each promoter region for each patient.
#This first line below is necessary so that the function run in methylation will work - filters only for probes present in PRADmeth
probes.in.PRAD <- subset(probes.gr, names(probes.gr) %in% rownames(PRADmeth))
probes.in.proms <- splicejam::annotateGRfromGR(probes.in.PRAD, promoters.gr)
df.probes.proms <- as.data.frame(probes.in.proms)
df.probes.proms <- df.probes.proms[, c('seqnames', 'start', 'end', 'ID', 'ID_v1')]
names(df.probes.proms)[names(df.probes.proms) == "ID"] <- "probe"
names(df.probes.proms)[names(df.probes.proms) == "ID_v1"] <- "promoter.id"
df.probes.proms <- na.omit(df.probes.proms)
df.probes.proms <- subset(df.probes.proms, df.probes.proms$promoter.id %in% promoters$ID)
df.probes.proms.FINAL <- aggregate(df.probes.proms[,4], list(df.probes.proms[,5]), function(x) paste0(unique(x)))
names(df.probes.proms.FINAL)[names(df.probes.proms.FINAL) == "Group.1"] <- "promoter"
names(df.probes.proms.FINAL)[names(df.probes.proms.FINAL) == "x"] <- "probe"
promoter.regions <- splicejam::annotateGRfromGR(promoters.gr, regions)
df.promoter.regions <- data.frame(promoter.regions)
df.probes.proms.FINAL$region <- subset(df.promoter.regions$region, df.promoter.regions$ID %in% df.probes.proms.FINAL$promoter)
The final data frame created above has each promoter and then a list of the probes that are considered part of that promoter.
save(df.probes.regions.genes, file = '../data/Output/df_pairs')
save(df.probes.proms.FINAL, file = '../data/Output/promoter_probes')
sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid parallel stats4 stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] data.table_1.12.6
[2] RnBeads.hg19_1.14.0
[3] dplyr_0.8.3
[4] splicejam_<IP_ADDRESS>0
[5] RnBeads_2.0.1
[6] plyr_1.8.4
[7] methylumi_2.28.0
[8] minfi_1.28.4
[9] bumphunter_1.24.5
[10] locfit_1.5-9.1
[11] iterators_1.0.12
[12] foreach_1.5.1
[13] Biostrings_2.50.2
[14] XVector_0.22.0
[15] FDb.InfiniumMethylation.hg19_2.2.0
[16] org.Hs.eg.db_3.7.0
[17] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[18] GenomicFeatures_1.34.8
[19] AnnotationDbi_1.44.0
[20] reshape2_1.4.3
[21] scales_1.0.0
[22] illuminaio_0.24.0
[23] limma_3.38.3
[24] gridExtra_2.3
[25] gplots_3.0.3
[26] ggplot2_3.2.1
[27] fields_9.9
[28] maps_3.3.0
[29] spam_2.3-0
[30] dotCall64_1.0-0
[31] ff_2.2-14
[32] bit_1.1-14
[33] cluster_2.0.7-1
[34] MASS_7.3-51.1
[35] MultiAssayExperiment_1.8.3
[36] SummarizedExperiment_1.12.0
[37] DelayedArray_0.8.0
[38] BiocParallel_1.16.6
[39] matrixStats_0.55.0
[40] Biobase_2.42.0
[41] ELMER_2.6.3
[42] ELMER.data_2.6.0
[43] rtracklayer_1.42.2
[44] GenomicRanges_1.34.0
[45] GenomeInfoDb_1.18.2
[46] IRanges_2.16.0
[47] S4Vectors_0.20.1
[48] BiocGenerics_0.28.0
loaded via a namespace (and not attached):
[1] rappdirs_0.3.1 ggthemes_4.2.0
[3] R.methodsS3_1.7.1 pkgmaker_0.27
[5] tidyr_1.0.0 acepack_1.4.1
[7] bit64_0.9-8 knitr_1.25
[9] aroma.light_3.12.0 R.utils_2.9.0
[11] rpart_4.1-13 hwriter_1.3.2
[13] GEOquery_2.50.5 RCurl_1.96-0
[15] AnnotationFilter_1.6.0 doParallel_1.0.15
[17] generics_0.0.2 preprocessCore_1.44.0
[19] RSQLite_2.1.2 xml2_1.2.2
[21] httpuv_1.5.2 assertthat_0.2.1
[23] xfun_0.10 hms_0.5.1
[25] evaluate_0.14 promises_1.1.0
[27] progress_1.2.2 caTools_<IP_ADDRESS>
[29] dbplyr_1.4.2 km.ci_0.5-2
[31] DBI_1.0.0 geneplotter_1.60.0
[33] htmlwidgets_1.5.1 reshape_0.8.8
[35] EDASeq_2.16.3 matlab_1.0.2
[37] purrr_0.3.3 selectr_0.4-1
[39] ggpubr_0.2.3 backports_1.1.5
[41] annotate_1.60.1 biomaRt_2.41.9
[43] vctrs_0.2.0 ensembldb_2.6.8
[45] withr_2.1.2 Gviz_1.26.5
[47] BSgenome_1.50.0 checkmate_1.9.4
[49] GenomicAlignments_1.18.1 prettyunits_1.0.2
[51] mclust_5.4.5 lazyeval_0.2.2
[53] crayon_1.3.4 genefilter_1.64.0
[55] edgeR_3.24.3 pkgconfig_2.0.3
[57] nlme_3.1-137 ProtGenerics_1.14.0
[59] nnet_7.3-12 rlang_0.4.0
[61] lifecycle_0.1.0 downloader_0.4
[63] registry_0.5-1 BiocFileCache_1.6.0
[65] dichromat_2.0-1 rprojroot_1.3-2
[67] rngtools_1.4 base64_2.0
[69] Matrix_1.2-15 KMsurv_0.1-5
[71] Rhdf5lib_1.4.3 zoo_1.8-7
[73] base64enc_0.1-4 whisker_0.4
[75] GlobalOptions_0.1.1 viridisLite_0.3.0
[77] rjson_0.2.20 shinydashboard_0.7.1
[79] bitops_1.0-6 R.oo_1.22.0
[81] ConsensusClusterPlus_1.46.0 KernSmooth_2.23-15
[83] blob_1.2.0 DelayedMatrixStats_1.4.0
[85] TCGAbiolinks_2.13.6 workflowr_1.5.0
[87] doRNG_1.7.1 shape_1.4.4
[89] stringr_1.4.0 shinydashboardPlus_<IP_ADDRESS>00
[91] nor1mix_1.3-0 ShortRead_1.40.0
[93] readr_1.3.1 ggsignif_0.6.0
[95] memoise_1.1.0 magrittr_1.5
[97] bibtex_0.4.2 gdata_2.18.0
[99] zlibbioc_1.28.0 compiler_3.5.2
[101] RColorBrewer_1.1-2 Rsamtools_1.34.1
[103] htmlTable_1.13.2 Formula_1.2-3
[105] mgcv_1.8-26 tidyselect_0.2.5
[107] stringi_1.4.3 yaml_2.2.0
[109] askpass_1.1 latticeExtra_0.6-28
[111] ggrepel_0.8.1 survMisc_0.5.5
[113] VariantAnnotation_1.28.13 tools_3.5.2
[115] circlize_0.4.8 rstudioapi_0.10
[117] foreign_0.8-71 git2r_0.26.1
[119] digest_0.6.22 shiny_1.4.0
[121] quadprog_1.5-7 Rcpp_1.0.2
[123] siggenes_1.56.0 broom_0.5.2
[125] later_1.0.0 shinyWidgets_0.4.9
[127] httr_1.4.1 survminer_0.4.6
[129] jamba_<IP_ADDRESS>0 biovizBase_1.30.1
[131] ComplexHeatmap_1.20.0 colorspace_1.4-2
[133] rvest_0.3.4 XML_3.99-0
[135] fs_1.3.1 splines_3.5.2
[137] multtest_2.38.0 plotly_4.9.0
[139] xtable_1.8-5 jsonlite_1.6
[141] zeallot_0.1.0 R6_2.4.0
[143] Hmisc_4.2-0 mime_0.7.1
[145] pillar_1.4.2 htmltools_0.4.0
[147] fastmap_1.0.1 glue_1.3.1
[149] DESeq_1.34.1 beanplot_1.2
[151] codetools_0.2-15 lattice_0.20-38
[153] tibble_2.1.3 sva_3.30.1
[155] curl_4.2 gtools_3.8.1
[157] openssl_1.4.1 survival_2.43-3
[159] rmarkdown_1.16 munsell_0.5.0
[161] GetoptLong_0.1.7 rhdf5_2.26.2
[163] GenomeInfoDbData_1.2.0 HDF5Array_1.10.1
[165] gtable_0.3.0


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