2008:Orion:Report - Revision history

Mark at 02:32, 20 February 2008

2008-02-20T02:32:55Z

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	=CSI Academy Concerto Portal Development=		=CSI Academy Concerto Portal Development=

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	Department of Electrical and Computer Engineering, University of Auckland.		Department of Electrical and Computer Engineering, University of Auckland.
	mgar059@ec.auckland.ac.nz		mgar059@ec.auckland.ac.nz
	<div>		</div>


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	Figure 2: Eclipse JUnit Plugin		Figure 2: Eclipse JUnit Plugin
	Once we had modified Concerto to be largely generic, we ran the unit tests to ensure none of the functionality was broken. The unit tests were broken up into suites and each suite tested a package of the code base. Many bugs were found, such as problems with ‘preDelete’ and ‘equals’ methods, class cast exceptions from adding generics, and there were even places where changing from an iterator to an enhanced for loop lost some logic. Examples of this last point include the use of an incrementing variable i.e. i++, as well as a standard iterator in the loop constructor, as well as ‘resolveRefrence’ calls. Usually a loop would have only one value, which changes for each iteration of a loop. In Concerto Portal there exist loops which make use of an incrementing loop count as an iterator passes over a list. These were easy to miss when refactoring (ergo the added visibility of this behaviour is one of the benefits of refactoring,) and the unit tests helped us to catch these mistakes.		Once we had modified Concerto to be largely generic, we ran the unit tests to ensure none of the functionality was broken. The unit tests were broken up into suites and each suite tested a package of the code base. Many bugs were found, such as problems with ‘preDelete’ and ‘equals’ methods, class cast exceptions from adding generics, and there were even places where changing from an iterator to an enhanced for loop lost some logic. Examples of this last point include the use of an incrementing variable i.e. i++, as well as a standard iterator in the loop constructor, as well as ‘resolveRefrence’ calls. Usually a loop would have only one value, which changes for each iteration of a loop. In Concerto Portal there exist loops which make use of an incrementing loop count as an iterator passes over a list. These were easy to miss when refactoring (ergo the added visibility of this behaviour is one of the benefits of refactoring,) and the unit tests helped us to catch these mistakes.

	===5.2. JUnit and TestNG===		===5.2. JUnit and TestNG===
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	A major benefit from this was the ability to access the repository from within eclipse. We used an Eclipse plugin called Subclipse.		A major benefit from this was the ability to access the repository from within eclipse. We used an Eclipse plugin called Subclipse.
	Figure 4: Eclipse Subclipse Plugin		Figure 4: Eclipse Subclipse Plugin
	Subclipse allowed us to compare the changes we made with previous versions in the repository. These changes would be highlighted and we could easily see if we had lost some code in the changes or allow us to revive methods we had removed.		Subclipse allowed us to compare the changes we made with previous versions in the repository. These changes would be highlighted and we could easily see if we had lost some code in the changes or allow us to revive methods we had removed.

	===6.7. Orion Intranet===		===6.7. Orion Intranet===
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	Zimbra is open source email server software which caters for email access and meeting or document collaboration [10].		Zimbra is open source email server software which caters for email access and meeting or document collaboration [10].
	Figure 5: Zimbra		Figure 5: Zimbra
	We used Zimbra to organise meeting times with our industry mentor, and it would notify us about events such as the monthly Concerto Group meetings.		We used Zimbra to organise meeting times with our industry mentor, and it would notify us about events such as the monthly Concerto Group meetings.

	====6.7.2. Confluence====		====6.7.2. Confluence====
	Orion health has a great wiki culture. All the information from the development teams and management are available and regularly updated on a Confluence wiki.		Orion health has a great wiki culture. All the information from the development teams and management are available and regularly updated on a Confluence wiki.
	Figure 6: Confluence Wiki		Figure 6: Confluence Wiki
	By documenting all the work that is done in the wiki, anyone within the company may, comment on or improve ideas. We found the wiki (or Woki, Where Orion Keeps Information) useful for understanding the tools and frameworks we used, as well as how to fix problems we came across which had been encountered by others.		By documenting all the work that is done in the wiki, anyone within the company may, comment on or improve ideas. We found the wiki (or Woki, Where Orion Keeps Information) useful for understanding the tools and frameworks we used, as well as how to fix problems we came across which had been encountered by others.

	====6.7.3. Jira====		====6.7.3. Jira====
	Jira is an issue and bug tracking portal, which Orion Health uses to assign units of work. Much of the development was focused towards resolving and managing tickets which had been raised in Jira.		Jira is an issue and bug tracking portal, which Orion Health uses to assign units of work. Much of the development was focused towards resolving and managing tickets which had been raised in Jira.
	Figure 7: Jira Bug Tracking Portal		Figure 7: Jira Bug Tracking Portal
	We used Jira to find out information on problems we were trying to fix, such as removing interfaces from the Concerto Portal. We also used Jira for issues such as requesting a product license for use while working on Concerto.		We used Jira to find out information on problems we were trying to fix, such as removing interfaces from the Concerto Portal. We also used Jira for issues such as requesting a product license for use while working on Concerto.

	==7. Conclusion==		==7. Conclusion==

Mark at 02:29, 20 February 2008

2008-02-20T02:29:55Z

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Mark at 02:01, 20 February 2008

2008-02-20T02:01:43Z

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Mark at 22:01, 19 February 2008

2008-02-19T22:01:32Z

← Older revision		Revision as of 22:01, 19 February 2008
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	Concerto Portal is one of a few software products produced by Orion Health, which make up a software solution for organising hospital information systems. Concerto Portal is a web-based application written in Java. Many hospitals have a range of programs and databases they use, from looking up patients x-rays, lab results, or immunisation records. Each of these programs may have to be run separately and requite a different login. Not only is this a hassle, but this can be slow and lives are literally at risk. Concerto Portal acts as a centralised interface for logging in and using these different systems.		Concerto Portal is one of a few software products produced by Orion Health, which make up a software solution for organising hospital information systems. Concerto Portal is a web-based application written in Java. Many hospitals have a range of programs and databases they use, from looking up patients x-rays, lab results, or immunisation records. Each of these programs may have to be run separately and requite a different login. Not only is this a hassle, but this can be slow and lives are literally at risk. Concerto Portal acts as a centralised interface for logging in and using these different systems.

			Figure 1: Concerto Portal 6.6.3

	With Concerto, clinicians or doctors can log in to the system once, and the authentication can be shared amongst the different medical applications that user has access too. Where in the past, a clinician may have had to search for a patient on one system to get a few details such as their medical history, and then switch to a different system to find their lab results, concerto can allow the clinician to search for the patient once and can switch between the patients documents and lab results without having to switch programs. Concerto also provides a consistent interface between these applications, which make finding information faster and more intuitive. Concerto even supports messages between users of the system and the interface can be customised to the specific needs of each hospital and user.		With Concerto, clinicians or doctors can log in to the system once, and the authentication can be shared amongst the different medical applications that user has access too. Where in the past, a clinician may have had to search for a patient on one system to get a few details such as their medical history, and then switch to a different system to find their lab results, concerto can allow the clinician to search for the patient once and can switch between the patients documents and lab results without having to switch programs. Concerto also provides a consistent interface between these applications, which make finding information faster and more intuitive. Concerto even supports messages between users of the system and the interface can be customised to the specific needs of each hospital and user.
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	Other minor changes we made to the Concerto code base includes: moving blocks of code, such as the ‘equals’ method, up the class definition hierarchy so that a single super class could implement equals. This would then be inherited by all child classes and removed some duplication of code. This also means that if the equals method was to be changed, it would only have to be modified in one place and all the child classes would be changed too. Unfortunately, we found that due to the desired behaviour of the ‘equals’ method, where it only compares objects of the same class, the ‘equals’ methods did have to be re-implemented in many child classes.		Other minor changes we made to the Concerto code base includes: moving blocks of code, such as the ‘equals’ method, up the class definition hierarchy so that a single super class could implement equals. This would then be inherited by all child classes and removed some duplication of code. This also means that if the equals method was to be changed, it would only have to be modified in one place and all the child classes would be changed too. Unfortunately, we found that due to the desired behaviour of the ‘equals’ method, where it only compares objects of the same class, the ‘equals’ methods did have to be re-implemented in many child classes.

	Annotations were automatically added where methods overrode super class methods. An example of this ~~being~~ the ‘equals’ method again. Another place changes had to be made were in the ‘preDelete’ methods. These methods ensure that when an object, such as a user on the system, is deleted, every object belonging to that user is deleted before the user is deleted. ~~This came about due~~ to ~~a change in~~ the structure ~~of all the objects which are persisted~~ to the ~~database. This method was also~~ reverted to ~~its~~ original implementation ~~eventually~~.		Annotations, with the use of source formatting and styling templates in Eclipse, were automatically added where methods overrode super class methods. An example of this is the ‘equals’ method again. An ‘@Override’ was added above the method signature to signify that the method had to override a defined method from a super class.

			Another place changes had to be made were in the ‘preDelete’ methods. These methods ensure that when an object, such as a user on the system, is deleted, every object belonging to that user is deleted before the user is deleted. When we made changes to part of the class structure, these methods stopped functioning as they were expected to, and had to be altered. As we made further changes to the code base, we eventually reverted these methods to their original implementation.

	4.2. Portal Interface Removal		4.2. Portal Interface Removal
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	5.1. Unit tests		5.1. Unit tests

	A significant amount of our time was spent running unit tests and tracking down the specific errors they found. The Concerto Portal has suites of tests written in JUnit. JUnit is a unit testing framework for Java. Once we had modified concerto to be largely generic, we ran the unit tests to ensure none of the functionality was broken. The unit tests were broken up into suites and each suite tested a package of the code base. Many bugs were found, such as problems with ‘preDelete’ and ‘equals’ methods, class cast exceptions from adding generics, and there were even places where changing from an iterator to an enhanced for loop lost some logic. Examples include the use of an incrementing variable i.e. i++, in the loop constructor, as well as ‘resolveRefrence’ calls. Usually a loop would have only one value which changes for each iteration of a loop. In Concerto Portal there exist loops which make use of an incrementing loop count as an iterator passes over a list. These were easy to miss when refactoring (As such the added visibility of this behaviour is one of the benefits of refactoring,) and the unit tests helped us to catch these mistakes.		A significant amount of our time was spent running unit tests and tracking down the specific errors they found. The Concerto Portal has suites of tests written in JUnit. JUnit is a unit testing framework for Java.

			Figure 2: Eclipse JUnit Plugin
			Once we had modified concerto to be largely generic, we ran the unit tests to ensure none of the functionality was broken. The unit tests were broken up into suites and each suite tested a package of the code base. Many bugs were found, such as problems with ‘preDelete’ and ‘equals’ methods, class cast exceptions from adding generics, and there were even places where changing from an iterator to an enhanced for loop lost some logic. Examples include the use of an incrementing variable i.e. i++, in the loop constructor, as well as ‘resolveRefrence’ calls. Usually a loop would have only one value which changes for each iteration of a loop. In Concerto Portal there exist loops which make use of an incrementing loop count as an iterator passes over a list. These were easy to miss when refactoring (As such the added visibility of this behaviour is one of the benefits of refactoring,) and the unit tests helped us to catch these mistakes.

	5.2. JUnit and TestNG		5.2. JUnit and TestNG
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	6.2. Eclipse		6.2. Eclipse

	Eclipse is an Integrated Development Environment for Java, which was originally created by IBM. It is now an open source tool, which is widely used and supported. We used it extensively throughout our work at Orion Health. We used eclipse to identify parts of the code base which needed refactoring. Eclipse generates a list of compiler warnings that identify what parts of code could be potentially unsafe and where generics could be added, and even underlines the specific parts of the code. There was the possibility for eclipse to attempt automatic refactoring, however this was largely not useful. There are a wide range of keyboard shortcuts and an inbuilt debugging interface that was useful. From within eclipse we could compile and run Concerto, and even the ruby WATFO framework and tests.		Eclipse is an Integrated Development Environment for Java, which was originally created by IBM.
			Figure 3: Eclipse 3.3 IDE
			Eclipse is now an open source tool, which is widely used and supported. We used it extensively throughout our work at Orion Health. We used eclipse to identify parts of the code base which needed refactoring. Eclipse generates a list of compiler warnings that identify what parts of code could be potentially unsafe and where generics could be added, and even underlines the specific parts of the code. There was the possibility for eclipse to attempt automatic refactoring, however this was largely not useful. There are a wide range of keyboard shortcuts and an inbuilt debugging interface that was useful. From within eclipse we could compile and run Concerto, and even the ruby WATFO framework and tests.

	6.2.1. Ant		6.2.1. Ant
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	The Concerto Portal code base is stored and controlled by a subversion repository. This allowed us to synchronise the changes we were making in different areas of the code and work on it simultaneously.		The Concerto Portal code base is stored and controlled by a subversion repository. This allowed us to synchronise the changes we were making in different areas of the code and work on it simultaneously.

	A major benefit from this was the ability to access the repository from within eclipse. We used an Eclipse plugin called Subclipse. Subclipse allowed us to compare the changes we made with previous versions in the repository. These changes would be highlighted and we could easily see if we had lost some code in the changes or allow us to revive methods we had removed.		A major benefit from this was the ability to access the repository from within eclipse. We used an Eclipse plugin called Subclipse.
			Figure 4: Subclipse Plugin
			Subclipse allowed us to compare the changes we made with previous versions in the repository. These changes would be highlighted and we could easily see if we had lost some code in the changes or allow us to revive methods we had removed.

	6.7. Orion Intranet		6.7. Orion Intranet
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	6.7.1. Zimbra		6.7.1. Zimbra
	Zimbra is open source email server software which caters for email access and meeting or document collaboration. We used Zimbra to organise meeting times with our industry mentor, and it would notify us about events such as the monthly Concerto Group meetings.		Zimbra is open source email server software which caters for email access and meeting or document collaboration.
			Figure 5: Zimbra
			We used Zimbra to organise meeting times with our industry mentor, and it would notify us about events such as the monthly Concerto Group meetings.

	6.7.2. Confluence		6.7.2. Confluence
	Orion health has a great wiki culture. All the information from the development teams and management are available and regularly updated on a Confluence wiki. By documenting all the work that is done in the wiki, anyone within the company may, comment on or improve ideas. We found the wiki (or Woki, Where Orion Keeps Information) useful for understanding the tools and frameworks we used, as well as how to fix problems we came across which had been encountered by others.		Orion health has a great wiki culture. All the information from the development teams and management are available and regularly updated on a Confluence wiki.
			Figure 6: Confluence Wiki
			By documenting all the work that is done in the wiki, anyone within the company may, comment on or improve ideas. We found the wiki (or Woki, Where Orion Keeps Information) useful for understanding the tools and frameworks we used, as well as how to fix problems we came across which had been encountered by others.

	6.7.3. Jira		6.7.3. Jira
	Jira is an issue and bug tracking portal, which Orion Health uses to assign units of work. Much of the development was focused towards resolving and managing tickets which had been raised in Jira. We used Jira to find out information on problems we were trying to fix, such as removing interfaces from the Concerto Portal. We also used Jira for issues such as requesting a product license for use while working on Concerto.		Jira is an issue and bug tracking portal, which Orion Health uses to assign units of work. Much of the development was focused towards resolving and managing tickets which had been raised in Jira.
			Figure 7: Jira Bug Tracking Portal
			We used Jira to find out information on problems we were trying to fix, such as removing interfaces from the Concerto Portal. We also used Jira for issues such as requesting a product license for use while working on Concerto.

	7. Conclusion		7. Conclusion
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	8. Acknowledgements		8. Acknowledgements

	I would like to thank ~~specifically;~~		I would like to specifically thank:
	Nicholas Irvine (Second Intern on this project)		· Nicholas Irvine (Second Intern on this project).
	Simon Leigh (Concerto Portal Development Team Lead)		· Simon Leigh (Concerto Portal Development Team Lead).
	Dr. Christof Lutteroth (Academic mentor)		· Dr. Christof Lutteroth (Academic mentor).
	Richard Li (Project Manager)		· Richard Li (Project Manager).
	Orion Health		· Orion Health.
	CSI Academy		· CSI Academy.

	9. References		9. References

Mark at 21:32, 19 February 2008

2008-02-19T21:32:58Z

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Mark at 03:52, 19 February 2008

2008-02-19T03:52:38Z

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Mark at 03:21, 19 February 2008

2008-02-19T03:21:22Z

← Older revision		Revision as of 03:21, 19 February 2008
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	6.4. JMX		6.4. JMX
	Concerto is designed to work with multiple different systems. JMX allows administrators to connect to a running Concerto instance directly and manage the system. When concerto starts up it goes through various stages or operability. It may not completely start up if it does not have a fully set up database for example. JMX is used to allow a connection into concerto for managing it, if it has not successfully started. We used JMX to set up the database to get concerto into a runnable state.		Concerto is designed to work with multiple different systems. JMX or Java Management Extensions, allows administrators to connect to a running Concerto instance directly and manage the system. When concerto starts up it goes through various stages or operability. It may not completely start up if it does not have a fully set up database for example. JMX is used to allow a connection into concerto for managing it, if it has not successfully started. We used JMX to set up the database to get concerto into a runnable state.

	6.6. Subversion		6.5. Subversion
	The Concerto Portal code base is stored and controlled by a subversion repository. This allowed us to synchronise the changes we were making in different areas of the code and work on it simultaneously.		The Concerto Portal code base is stored and controlled by a subversion repository. This allowed us to synchronise the changes we were making in different areas of the code and work on it simultaneously.
	A major benefit from this was the ability to access the repository from within eclipse. ~~The~~ Subclipse it allowed us to compare the changes we made with previous versions in the repository. These changes ~~were~~ highlighted and we could easily see if we had lost some code in the changes or revive methods we had removed.		A major benefit from this was the ability to access the repository from within eclipse. We used an Eclipse plugin called Subclipse. Subclipse allowed us to compare the changes we made with previous versions in the repository. These changes would be highlighted and we could easily see if we had lost some code in the changes or allow us to revive methods we had removed.

	6.7. Orion Intranet		6.7. Orion Intranet
	~~Within~~ Orion ~~there are widely used networking~~ tools for communication and ~~management available over the local intranet~~.		Orion has a company wide intranet with tools for communication, getting information, management, tracking bugs, and accessing code.

	6.7.1. Zimbra		6.7.1. Zimbra
	Zimbra is open source email server software which caters for email access and meeting or document collaboration.		Zimbra is open source email server software which caters for email access and meeting or document collaboration. We used Zimbra to organise meeting times with our industry mentor, and it would notify us about events such as the monthly Concerto Group meetings.
	6.7.2. Confluence		6.7.2. Confluence
			Orion health has a great wiki culture. All the information from the development teams and management are available and regularly updated. By documenting all the work that is done in the wiki, anyone within the company may,
	Same as the uni wiki we are using for CSI.		Same as the uni wiki we are using for CSI.
	First week, getting up to speed with the products.		First week, getting up to speed with the products.

Mark at 02:47, 19 February 2008

2008-02-19T02:47:02Z

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Mark at 23:43, 18 February 2008

2008-02-18T23:43:46Z

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Mark at 02:50, 18 February 2008

2008-02-18T02:50:48Z

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