SVN & google code hosting More on GSP Including third parties libraries Ajax Runtime environment Domains

1. Groovy: Efficiency Oriented Programming
Lecture 10
Master Proteomics & Bioinformatics - University of Geneva
Alexandre Masselot - summer 2011

2. Agenda
‣ SVN & google code hosting
‣ More on GSP
‣ Including third parties libraries
‣ Ajax
‣ Runtime environment
‣ Domains

3. SCM
‣ Code evolve in time

4. SCM
‣ Code evolve in time
‣ Source code is shared

5. SCM
‣ Code evolve in time
‣ Source code is shared
‣ Source Code Management system host code + versioning

6. SCM
‣ Code evolve in time
‣ Source code is shared
‣ Source Code Management system host code + versioning
‣ Many solutions exist: CVS, SVN, GIT, SourceSafe...

7. SCM
‣ Code evolve in time
‣ Source code is shared
‣ Source Code Management system host code + versioning
‣ Many solutions exist: CVS, SVN, GIT, SourceSafe...
‣ SVN is a client/server solution

8. SCM
‣ Code evolve in time
‣ Source code is shared
‣ Source Code Management system host code + versioning
‣ Many solutions exist: CVS, SVN, GIT, SourceSafe...
‣ SVN is a client/server solution
‣ Server can be in-house

9. SCM
‣ Code evolve in time
‣ Source code is shared
‣ Source Code Management system host code + versioning
‣ Many solutions exist: CVS, SVN, GIT, SourceSafe...
‣ SVN is a client/server solution
‣ Server can be in-house
‣ Free solution for open source
http://code.google.com/hosting/

10. make an google account

12. Create Project
Project name: geop-demo
Project summary: A demo project for GEOP course
Project description: geop demo code
Version control system: Subversion
Source code license: New BSD License
Use a separate content license:
license...
Project labels:
Create project...
Project name must start with a lowercase letter, followed by lowercase letters, digits, and dashes, with no
spaces. This will be part of your project's URL and cannot be changed later.
Project summary will be shown whenever the project's name is displayed.
Project description is the main content of your project's home page. You may use wiki markup.
Version control system selects the type of your project's repository. Learn more.
Licenses determine how others may build upon your work. Code and documentation may be distributed under
separate licenses.
Project labels help classify your project so others can easily find it or browse projects by label.

13. Google proposes command line commands
We’ll see how to integrate svn into eclipse

15. Command-line access
If you plan to make changes, use this command to check out the code as yourself using HTTPS:
# Project members authenticate over HTTPS to allow committing changes.
svn checkout https://geop-demo.googlecode.com/svn/trunk/ geop-demo --username alexandre.masselot
When prompted, enter your generated googlecode.com password.
Use this command to anonymously check out the latest project source code:
# Non-members may check out a read-only working copy anonymously over HTTP.
svn checkout http://geop-demo.googlecode.com/svn/trunk/ geop-demo-read-only
GUI and IDE access
This project's Subversion repository may be accessed using many different client programs and plug-ins. See your client's
documentation for more information.

16. Google code offers for “free”
‣ SVN repository

17. Google code offers for “free”
‣ SVN repository
‣ Managing contributors to a project

18. Google code offers for “free”
‣ SVN repository
‣ Managing contributors to a project
‣ Wiki

19. Google code offers for “free”
‣ SVN repository
‣ Managing contributors to a project
‣ Wiki
‣ Ticketing system

20. Google code offers for “free”
‣ SVN repository
‣ Managing contributors to a project
‣ Wiki
‣ Ticketing system
‣ Bug reporting

21. Google code offers for “free”
‣ SVN repository
‣ Managing contributors to a project
‣ Wiki
‣ Ticketing system
‣ Bug reporting
‣ Visibility

22. Google code hosting
⇒
your code is open source

23. SVN: eclipse or command line

24. Installing svn in Eclipse
‣ Help > dashboard > extension
- Subversion (subclipse)

25. Installing svn in Eclipse
‣ Help > dashboard > extension
- Subversion (subclipse)
‣ Or command line: installed by default or
- sudo apt-get install subversion

26. Eclipse: connecting to the SVN repository
‣ menu Window
- > open perspective
- > SVN repository exploring

27. Eclipse: connecting to the SVN repository
‣ menu Window
- > open perspective
- > SVN repository exploring
‣ view SVN repositories
- > right click
- > new repository location
- https://geop-demo.googlecode.com/svn

31. Sharing an existing project to your google code account

32. Sharing an existing project to your google code account
‣ Perspective java

33. Sharing an existing project to your google code account
‣ Perspective java
‣ project right-click
- > team
- > share project
- use specifier folder name
trunk/your.project.name

34. ‣ username & password
from google page
‣ save password
check box

35. Commit the project
‣ At this stage, the project is only created on the remote server
- check with SVN repository exploring perspective
- or browse source code from google page

36. Commit the project
‣ At this stage, the project is only created on the remote server
- check with SVN repository exploring perspective
- or browse source code from google page
‣ Mark generated file & folder to be ignored from svn
- e.g. target/

37. Commit the project
‣ At this stage, the project is only created on the remote server
- check with SVN repository exploring perspective
- or browse source code from google page
‣ Mark generated file & folder to be ignored from svn
- e.g. target/
‣ Right-click > team > add to svn:ignore

40. All eclipse functionalities
can be replaced by shell commands

41. SVN command line: share project
‣ Import original project demo.svn to the repository
‣ cd workspace directory
svn import -m “initial import” --non-recursive demo.svn
https://geop-demo.googlecode.com/svn/trunk/demo.svn
‣ Directory itself is not imported, so checkout (with force)
svn checkout --force https://geop-demo.googlecode.com/svn/
trunk/demo.svn

42. SVN command line: share project (cont’d)
cd demo.svn
‣ Add target/ directory to svn:ignore
svn propset svn:ignore target .
‣ Add other directories to svn
svn add $(ls | grep -v target)
‣ Commit files
svn commit -m "adding all initial files"
‣ Back to eclipse, F5 (refresh in package explorer view)

43. Browse your project

44. From google code source page
25

45. SVN for a daily use

46. SVN for a daily use
minutely

47. SVN: flow use
‣ Checkout out or share an existing project to contribute

48. SVN: flow use
‣ Checkout out or share an existing project to contribute
‣ Commit changes to the repository

49. SVN: flow use
‣ Checkout out or share an existing project to contribute
‣ Commit changes to the repository
‣ Update changes from repository

50. SVN: flow use
‣ Checkout out or share an existing project to contribute
‣ Commit changes to the repository
‣ Update changes from repository
‣ Eclipse:
- select project
- > right-click
- > team
- > Synchronize with repository
- commit/update/manage conflict

51. SVN: flow use (cont’d)
‣ Command line
svn status
svn update
svn commit -m “my message to describe changes”

52. Commit/update often

53. SVN is more
‣ History

54. SVN is more
‣ History
‣ See contribution from others

55. SVN is more
‣ History
‣ See contribution from others
‣ Tag / branch versions

56. SVN is more
‣ History
‣ See contribution from others
‣ Tag / branch versions
‣ Conflict resolution

57. SVN is more
‣ History
‣ See contribution from others
‣ Tag / branch versions
‣ Conflict resolution
‣ Continuous integration / testing on dedicated server

58. SVN is more
‣ History
‣ See contribution from others
‣ Tag / branch versions
‣ Conflict resolution
‣ Continuous integration / testing on dedicated server
‣ File locking :(

59. SVN is more
‣ History
‣ See contribution from others
‣ Tag / branch versions
‣ Conflict resolution
‣ Continuous integration / testing on dedicated server
‣ File locking :(
‣ Integration with tickets

60. SVN is more
‣ History
‣ See contribution from others
‣ Tag / branch versions
‣ Conflict resolution
‣ Continuous integration / testing on dedicated server
‣ File locking :(
‣ Integration with tickets
‣ Windows integration: http://tortoisesvn.tigris.org/

61. Back to grails... and proteins isoforms

62. Problem: uniprot AC ➙ isoform list
in a web application

63. Grails: including a third parties libraries
‣ Library is available as a jar (export ➙ .jar)

64. Grails: including a third parties libraries
‣ Library is available as a jar (export ➙ .jar)
‣ Copy jar in lib/

65. Grails: including a third parties libraries
‣ Library is available as a jar (export ➙ .jar)
‣ Copy jar in lib/
‣ For eclipse completion
- right-click
- build path
- add to build path

66. Get is forms for ac (00:44:01.975)
Q70Z44
List
>Q70Z44-1
MQKHSPGPPALALLSQSLLTTGNGDTLIINCPGFGQHRVDPAAFQAVFDRKAIGPVTNYS
VATHVNISFTLSAIWNCYSRIHTFNCHHARPWHNQFVQWNPDECGGIKKSGMATENLWLS
DVFIEESVDQTPAGLMASMSIVKATSNTISQCGWSASANWTPSISPSMDRARAWRRMSRS
FQIHHRTSFRTRREWVLLGIQKRTIKVTVATNQYEQAIFHVAIRRRCRPSPYVVNFLVPS
GILIAIDALSFYLPLESGNCAPFKMTVLLGYSVFLLMMNDLLPATSTSSHASLVAPLALM
QTPLPAGVYFALCLSLMVGSLLETIFITHLLHVATTQPLPLPRWLHSLLLHCTGQGRCCP
TAPQKGNKGPGLTPTHLPGVKEPEVSAGQMPGPGEAELTGGSEWTRAQREHEAQKQHSVE
LWVQFSHAMDALLFRLYLLFMASSIITVICLWNT
>Q70Z44-2
MASMSIVKATSNTISQCGWSASANWTPSISPSMDRAERSPSALSPTQVAIRRRCRPSPYV
VNFLVPSGILIAIDALSFYLPLESGNCAPFKMTVLLGYSVFLLMMNDLLPATSTSSHASL
VRPHPSRDQKRGVYFALCLSLMVGSLLETIFITHLLHVATTQPLPLPRWLHSLLLHCTGQ
GRCCPTAPQKGNKGPGLTPTHLPGVKEPEVSAGQMPGPGEAELTGGSEWTRAQREHEAQK
QHSVELWVQFSHAMDALLFRLYLLFMASSIITVICLWNT

67. Isoforms_v1 -> v5 same controller
different views (gsp)
for different rendering interaction

68. Isoforms_v1 -> v5 same controller
different views (gsp)
for different rendering interaction

69. Isoforms_vXController
⇒
views/isoforms_vX/ direcgtory with gsp’s

70. IsoformController_v?.groovy
def list = {
def ac=params.ac
def xml=new XmlSlurper()
.parseText("http://pir.uniprot.org/uniprot/$
{ac}.xml".toURL().text).entry
UniprotEntrySplicer splicer=[entryXml:xml]
def proteins=splicer.buildAllIsoforms().values() as
List
[proteins: proteins]
}

71. v1

72. isoforms_v1/list.gsp
<html>
<body>
<h2>Get is forms for ac (${String.format('%tH:%<tM:
%<tS.%<tL', new Date())})</h2>
<g:form action="list">
<g:textField name="ac" value="${params.ac}" />
<g:submitButton name="submit" />
</g:form>
<h3>List</h3>
<g:each in="${proteins}" var="prot">
<pre>
${prot}
</pre>
</g:each>
</body>
</html>

73. Problem: direct access to /list only

74. v2

75. v2

76. isoforms_v2: add index.gsp
<html>
<body>
<h1>Isoform list application</h1>
<h2>Get is forms for ac (${String.format('%tH:%<tM:
%<tS.%<tL', new Date())})</h2>
<g:form action="list">
<g:textField name="ac" value="${params.ac}" />
<g:submitButton name="submit" />
</g:form>
</body>
</html>

77. Problem: <g:form> is duplicated (DRY!)

78. isoform_v3: use template
‣ _form.gsp
<h2>Get is forms for ac (${String.format('%tH:%<tM:%<tS.
%<tL', new Date())})</h2>
<g:form action="list">
<g:textField name="ac" value="${params.ac}" />
<g:submitButton name="submit" />
</g:form>

79. isoform_v3: use template
‣ _form.gsp
<h2>Get is forms for ac (${String.format('%tH:%<tM:%<tS.
%<tL', new Date())})</h2>
<g:form action="list">
<g:textField name="ac" value="${params.ac}" />
<g:submitButton name="submit" />
</g:form>
‣ In index.gsp and list.gsp
<g:render template="form" />

80. isoform_v3: use template
‣ _form.gsp
<h2>Get is forms for ac (${String.format('%tH:%<tM:%<tS.
%<tL', new Date())})</h2>
<g:form action="list">
<g:textField name="ac" value="${params.ac}" />
<g:submitButton name="submit" />
</g:form>
‣ In index.gsp and list.gsp
<g:render template="form" />

81. Problem: all the page is reloaded totally

82. v4

83. Ajax: asynchronous load
web browser
Q70Z44 submit server
isoform/list
47

84. Ajax: asynchronous load
web browser
Q70Z44 submit server
isoform/list
47

85. Ajax: asynchronous load
web browser
Q70Z44 submit server
List isoform/list
>Q70Z44-1
MQKHSPGPPALALLSQSLLTTGNGDTLIINCPGFGQHRVDPAAFQAVFDRKAIGPVTNYS
VATHVNISFTLSAIWNCYSRIHTFNCHHARPWHNQFVQWNPDECGGIKKSGMATENLWLS
DVFIEESVDQTPAGLMASMSIVKATSNTISQCGWSASANWTPSISPSMDRARAWRRMSRS
FQIHHRTSFRTRREWVLLGIQKRTIKVTVATNQYEQAIFHVAIRRRCRPSPYVVNFLVPS
GILIAIDALSFYLPLESGNCAPFKMTVLLGYSVFLLMMNDLLPATSTSSHASLVAPLALM
QTPLPAGVYFALCLSLMVGSLLETIFITHLLHVATTQPLPLPRWLHSLLLHCTGQGRCCP
TAPQKGNKGPGLTPTHLPGVKEPEVSAGQMPGPGEAELTGGSEWTRAQREHEAQKQHSVE
LWVQFSHAMDALLFRLYLLFMASSIITVICLWNT
>Q70Z44-2
MASMSIVKATSNTISQCGWSASANWTPSISPSMDRAERSPSALSPTQVAIRRRCRPSPYV
VNFLVPSGILIAIDALSFYLPLESGNCAPFKMTVLLGYSVFLLMMNDLLPATSTSSHASL
VRPHPSRDQKRGVYFALCLSLMVGSLLETIFITHLLHVATTQPLPLPRWLHSLLLHCTGQ
GRCCPTAPQKGNKGPGLTPTHLPGVKEPEVSAGQMPGPGEAELTGGSEWTRAQREHEAQK
QHSVELWVQFSHAMDALLFRLYLLFMASSIITVICLWNT
47

86. isoform_v4/index.gsp
<html>
<head>
<g:javascript library="prototype" />
</head>
<body>
<h2>Get is forms for ac (${String.format('%tH:%<tM:
%<tS.%<tL', new Date())})</h2>
<!-- g:formRemote stands for an ajax form -->
<g:formRemote name="listForm" url="[action:'list']"
update="isoforms-list">
<g:textField name="ac" value="${params.ac}" />
<g:submitButton name="submit" />
</g:formRemote>
<!-- the target element of the form -->
<div id="isoforms-list"/>
</body>
</html>

87. isoform_v4/list.gsp
<h3>List</h3>
<g:each in="${proteins}" var="prot">
<pre>
${prot}
</pre>
</g:each>

88. Twitter 1

89. People post messages and follow others

90. database (domain)
+ controller (actions)
+ views (web)

91. Domain: Person & Message

92. Domain: bean definition + database storage

93. Person domain
‣ Create the database entry + bean class
grails create-domain-class Person
project > right-click > grails > create-domain-class
Person

94. Person domain
‣ Create the database entry + bean class
grails create-domain-class Person
project > right-click > grails > create-domain-class
Person
‣ Files created:
./grails-app/domain/eop/lec10/twitter/Person.groovy
./test/unit/eop/lec10/twitter/PersonTests.groovy

95. Person.groovy
‣ Created class
package eop.lec10.twitter
class Person {
static constraints = {
}
}

96. Person.groovy

97. Person.groovy
‣ Enriched with fields
package eop.lec10.twitter
class Person {
String username
String firstName
String lastName
String email
Date dateCreated
static constraints = {
}
}

98. run-app ⇒ database + table created

99. Web access: need controller + views

100. Scaffolding is pure magic

101. PersonController.groovy
create-controller Person

102. PersonController.groovy
create-controller Person
‣ grails-app/controller/PersonController.groovy:
package eop.lec10.twitter
class PersonController {
def scaffold = true
}

103. PersonController.groovy
create-controller Person
‣ grails-app/controller/PersonController.groovy:
package eop.lec10.twitter
class PersonController {
def scaffold = true
}
‣ scaffold generate all default action & view implicitely

104. PersonController.groovy
create-controller Person
‣ grails-app/controller/PersonController.groovy:
package eop.lec10.twitter
class PersonController {
def scaffold = true
}
‣ scaffold generate all default action & view implicitely

105. http://localhost:8080/eop.lec10.twitter/person
‣ Default url is redirected on the list page

106. http://localhost:8080/eop.lec10.twitter/person
‣ Default url is redirected on the list page

107. http://localhost:8080/eop.lec10.twitter/person
‣ Entering a new Person lucky luke

108. http://localhost:8080/eop.lec10.twitter/person
‣ Entering a new Person lucky luke

109. http://localhost:8080/eop.lec10.twitter/person
‣ Entering a new Person lucky luke

110. http://localhost:8080/eop.lec10.twitter/person

111. http://localhost:8080/eop.lec10.twitter/person
‣ Back to list
- view all
- edit
- delete
- sort

112. Domain constraints

113. Person.groovy
class Person {
String username
String firstName
String lastName
String email
Date dateCreated
//firstName is compulsory
//email field has an email format
//username cannot be null, is unique and is between 6
and 20 characters
static constraints = {
firstName(blank:false)
email(email:true, blank:false)
username(blank:false, unique:true,
matches:/w{6,20}/)
}
}