Eclipse tips Productive tip Two thoughts on code design Running a script standalone test case: build all isoforms & extract proteotypic peptides

1. Groovy: Efficiency Oriented Programming
Lecture 6
Master Proteomics & Bioinformatics - University of Geneva
Alexandre Masselot - summer 2011

2. Contents
‣ Eclipse tips
‣ Productive tip
‣ Two thoughts on code design
‣ Running a script standalone
‣ test case: build all isoforms & extract proteotypic peptides

3. The book of the day
‣ by Neal Ford
‣ Do’s and Don’t for programmer, from the
rookies to ol’timers...

4. Go productive: clipboard history
‣ Working with a computer induces a lot of cut/past (<ctrl>-C / <ctrl>-V)

5. Go productive: clipboard history
‣ Working with a computer induces a lot of cut/past (<ctrl>-C / <ctrl>-V)
‣ In practice, you often refer (or intent to refer) to a piece of text you cut a
few minutes ago

6. Go productive: clipboard history
‣ Working with a computer induces a lot of cut/past (<ctrl>-C / <ctrl>-V)
‣ In practice, you often refer (or intent to refer) to a piece of text you cut a
few minutes ago
‣ It is possible to use clipboard history (and <ctrl>-V’ offers to visit
history)
- mac OS: jumpcut
- ubuntu: parcellite
- windows: CLCL

7. Go productive: clipboard history
‣ Working with a computer induces a lot of cut/past (<ctrl>-C / <ctrl>-V)
‣ In practice, you often refer (or intent to refer) to a piece of text you cut a
few minutes ago
‣ It is possible to use clipboard history (and <ctrl>-V’ offers to visit
history)
- mac OS: jumpcut
- ubuntu: parcellite
- windows: CLCL
‣ What a big deal?
- such functionalities has been present in editors such as vi or x?emacs
for decades...

8. Eclipse tips

9. Eclipse tips
‣ create documentation for a method (filled with method parameters)
- place the cursor on the method name
- right button > source > generate comment
- or <ctrl>-<alt>-J
- documentation is ready to be exported in a html javadoc

10. Eclipse tips

11. Eclipse tips
‣ How to know where a method is called?
- place the cursor on the method declaration
- right button > open call hierarchy
- or <ctrl>-<alt>-H

12. DRY: Don’t Repeat Yourself
7

13. Code design: DRY
‣ <ctrl>-C / <ctrl>-V is the most common shortcut appealing to
duplicate a piece of “working” code into another part of the software

14. Code design: DRY
‣ Problems:

15. Code design: DRY
‣ Problems:
- harder to understand where a given action is coded,

16. Code design: DRY
‣ Problems:
- harder to understand where a given action is coded,
- hard to maintain bug.

17. Code design: DRY
‣ Fight against DRY:

18. Code design: DRY
‣ Fight against DRY:
- refactor your code continuously (test are there to ensure stability).

19. Code design: DRY
‣ Fight against DRY:
- refactor your code continuously (test are there to ensure stability).
- tackle duplication in your process at any level

20. Code design: DRY
‣ Fight against DRY:
- refactor your code continuously (test are there to ensure stability).
- tackle duplication in your process at any level
- time spent for factorizing process or code is almost never a waste

21. YAGNI: You Ain’t Gonna Need It
11

22. Code design: YAGNI
‣ A very common pitfall when writing code it to follow some enthusiasm and
imagine features that are (on the instant you imagine them):

23. Code design: YAGNI
‣ A very common pitfall when writing code it to follow some enthusiasm and
imagine features that are (on the instant you imagine them):
- very cool,

24. Code design: YAGNI
‣ A very common pitfall when writing code it to follow some enthusiasm and
imagine features that are (on the instant you imagine them):
- very cool,
- you have a bright idea on how to implement them,

25. Code design: YAGNI
‣ A very common pitfall when writing code it to follow some enthusiasm and
imagine features that are (on the instant you imagine them):
- very cool,
- you have a bright idea on how to implement them,
- even though they don’t answer a particular need at that time, you “feel”
they would be “cool to have in the future”

26. Code design: YAGNI
‣ Problems:

27. Code design: YAGNI
‣ Problems:
- the code get more complex, harder to maintain,

28. Code design: YAGNI
‣ Problems:
- the code get more complex, harder to maintain,
- in a few weeks of time, this feature won’t be of any use (but other will!)

29. Code design: YAGNI
‣ Fight YAGNI:

30. Code design: YAGNI
‣ Fight YAGNI:
- stick to your customer practical needs

31. Code design: YAGNI
‣ Fight YAGNI:
- stick to your customer practical needs
- pair programming is the most efficient way to tackle such situations

32. Groovy: running a script (outside the IDE)
‣ Programming goal is (often) to have a runnable program, outside the IDE

33. Groovy: running a script (outside the IDE)
‣ Programming goal is (often) to have a runnable program, outside the IDE
‣ Be able to deploy the program on another machine

34. Groovy: running a script (outside the IDE)
‣ Programming goal is (often) to have a runnable program, outside the IDE
‣ Be able to deploy the program on another machine
‣ First: install Groovy on the machine (apt-get install groovy etc.)

35. Groovy: running a script (outside the IDE)
‣ Programming goal is (often) to have a runnable program, outside the IDE
‣ Be able to deploy the program on another machine
‣ First: install Groovy on the machine (apt-get install groovy etc.)
‣ Let’s consider a simple script hw.groovy, stored in directory /some/path
println “hello, world”

36. Groovy: running a script (outside the IDE)
‣ Programming goal is (often) to have a runnable program, outside the IDE
‣ Be able to deploy the program on another machine
‣ First: install Groovy on the machine (apt-get install groovy etc.)
‣ Let’s consider a simple script hw.groovy, stored in directory /some/path
println “hello, world”
‣ launch the script from command line
groovy hw.groovy

37. Parsing command line arguments
‣ Runtime arguments are passed on the command line

38. Parsing command line arguments
‣ Runtime arguments are passed on the command line
‣ Defining the possible arguments
def cli = new CliBuilder(usage:'myscript.groovy [options]')
//binary argument -h or --help and usage text
cli.h(longOpt:'help', 'usage information')
//compulsory argument for -n or --name=<user name>
cli.n(longOpt:'name', argName:'user name', args:1,
required: true, 'some user to salute')
//facultative argument --int-value=<int>
cli.i(longOpt:'int-value', argName:'int', args:1,
'some integer value')

39. Parsing command line arguments (cont’d)
‣ Parsing the command line
def options = cli.parse(args)
if (!options) return

40. Parsing command line arguments (cont’d)
‣ Parsing the command line
def options = cli.parse(args)
if (!options) return
‣ Check --help
if (options.help) cli.usage()

41. Parsing command line arguments (cont’d)
‣ Parsing the command line
def options = cli.parse(args)
if (!options) return
‣ Check --help
if (options.help) cli.usage()
‣ Arguments usage:
println "Hello $options.name (${options['int-value']})"

42. Parsing command line arguments (cont’d)
‣ groovy myscript.groovy --help
usage: myscript.groovy [options]
-h,--help usage information
-i,--int-value <int> some integer value
-n,--name <user name> some user to salute

43. Parsing command line arguments (cont’d)
‣ groovy myscript.groovy --help
usage: myscript.groovy [options]
-h,--help usage information
-i,--int-value <int> some integer value
-n,--name <user name> some user to salute
‣ groovy myscript.groovy --name=alice --int-value=234
Hello alice (234)

44. Parsing command line arguments (cont’d)
‣ groovy myscript.groovy --help
usage: myscript.groovy [options]
-h,--help usage information
-i,--int-value <int> some integer value
-n,--name <user name> some user to salute
‣ groovy myscript.groovy --name=alice --int-value=234
Hello alice (234)
‣ More doc on http://groovy.codehaus.org/gapi/groovy/util/CliBuilder.html

45. Parsing command line arguments (cont’d)
‣ The whole script:
def cli = new CliBuilder(usage:'myscript.groovy [options]')
cli.h(longOpt:'help', 'usage information')
cli.n(longOpt:'name', argName:'user name', args:1,
required: true, 'some user to salute')
cli.i(longOpt:'int-value', argName:'int', args:1,
'some integer value')
def options = cli.parse(args)
if (!options) return
if (options.help) cli.usage()
println "Hello $options.name (${options['int-value']}) "

46. Running a script with a packaged library
‣ A script by itself is soon meaningless, it is often backed by a library of
packaged classes for doing the actual business

47. Running a script with a packaged library
‣ A script by itself is soon meaningless, it is often backed by a library of
packaged classes for doing the actual business
‣ The script is often the last assembly of coded (and tested) functionalities

48. Running a script with a packaged library
‣ A script by itself is soon meaningless, it is often backed by a library of
packaged classes for doing the actual business
‣ The script is often the last assembly of coded (and tested) functionalities
‣ Library is packaged as a jar (Java Archive) and the script is written on the
side, making calls to the archive

49. Running a script with a packaged library
‣ A script by itself is soon meaningless, it is often backed by a library of
packaged classes for doing the actual business
‣ The script is often the last assembly of coded (and tested) functionalities
‣ Library is packaged as a jar (Java Archive) and the script is written on the
side, making calls to the archive
‣ The jar if often the distributed part of a code

50. Running a script with a packaged library
‣ A script by itself is soon meaningless, it is often backed by a library of
packaged classes for doing the actual business
‣ The script is often the last assembly of coded (and tested) functionalities
‣ Library is packaged as a jar (Java Archive) and the script is written on the
side, making calls to the archive
‣ The jar if often the distributed part of a code
‣ The script varsplic.groovy uses the jar
import unige.mpb.eop.proteomics.uniprot.UniprotEntrySplicer
...
def xml=new XmlSlurper()
.parseText("http://pir.uniprot.org/uniprot/${ac}.xml"
.toURL().text)
.entry
UniprotEntrySplicer splicer=[entryXml:xml]
splicer.buildAllIsoforms().values().each{print it}

51. Eclipse: exporting a jar from the IDE
‣ A jar is an archive that contains at least the compiled classes

52. Eclipse: exporting a jar from the IDE
‣ A jar is an archive that contains at least the compiled classes
‣ Test classes are usually not exported

53. Eclipse: exporting a jar from the IDE
‣ A jar is an archive that contains at least the compiled classes
‣ Test classes are usually not exported
‣ Exporting from eclipse
- project > right button > export > java > jar

54. Eclipse: exporting a jar from the IDE
‣ A jar is an archive that contains at least the compiled classes
‣ Test classes are usually not exported
‣ Exporting from eclipse
- project > right button > export > java > jar
‣ A myfile.jar file is created

55. Eclipse: exporting a jar from the IDE
‣ A jar is an archive that contains at least the compiled classes
‣ Test classes are usually not exported
‣ Exporting from eclipse
- project > right button > export > java > jar
‣ A myfile.jar file is created

56. Eclipse: exporting a jar from ant
‣ Apache ant is a versatile tool for automatic software build process

57. Eclipse: exporting a jar from ant
‣ Apache ant is a versatile tool for automatic software build process
‣ It can be used to build a task: the build.xml (at project home directory)
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<project default="create_run_jar" name="Create Runnable Jar for Project
eop.lec6">
<targetname="create_run_jar">
<jar destfile="eop6.jar">
<fileset dir="bin">
<exclude name="**/*Test.class"/>
<exclude name="src/practicals/groovy/scripts/*"/>
</fileset>
</jar>
</target>
</project>

58. Eclipse: exporting a jar from ant
‣ Apache ant is a versatile tool for automatic software build process
‣ It can be used to build a task: the build.xml (at project home directory)
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<project default="create_run_jar" name="Create Runnable Jar for Project
eop.lec6">
<targetname="create_run_jar">
<jar destfile="eop6.jar">
<fileset dir="bin">
<exclude name="**/*Test.class"/>
<exclude name="src/practicals/groovy/scripts/*"/>
</fileset>
</jar>
</target>
</project>
‣ right button > run as > ant build

59. Eclipse: exporting a jar from ant
‣ Apache ant is a versatile tool for automatic software build process
‣ It can be used to build a task: the build.xml (at project home directory)
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<project default="create_run_jar" name="Create Runnable Jar for Project
eop.lec6">
<targetname="create_run_jar">
<jar destfile="eop6.jar">
<fileset dir="bin">
<exclude name="**/*Test.class"/>
<exclude name="src/practicals/groovy/scripts/*"/>
</fileset>
</jar>
</target>
</project>
‣ right button > run as > ant build
‣ <ctrl>-<alt>-X-Q

60. Eclipse: exporting a jar from ant
‣ Apache ant is a versatile tool for automatic software build process
‣ It can be used to build a task: the build.xml (at project home directory)
<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<project default="create_run_jar" name="Create Runnable Jar for Project
eop.lec6">
<targetname="create_run_jar">
<jar destfile="eop6.jar">
<fileset dir="bin">
<exclude name="**/*Test.class"/>
<exclude name="src/practicals/groovy/scripts/*"/>
</fileset>
</jar>
</target>
</project>
‣ right button > run as > ant build
‣ <ctrl>-<alt>-X-Q
‣ http://ant.apache.org/manual/tasksoverview.html

61. Executing a script with a jar library
‣ The script varsplic.groovy can reside anywhere
groovy -cp eop6.jar /path/to/varsplic.groovy --ac=Q70Z44

62. Executing a script with a jar library
‣ The script varsplic.groovy can reside anywhere
groovy -cp eop6.jar /path/to/varsplic.groovy --ac=Q70Z44
‣ Arguments following the script will be passed to the script args

63. Executing a script with a jar library
‣ The script varsplic.groovy can reside anywhere
groovy -cp eop6.jar /path/to/varsplic.groovy --ac=Q70Z44
‣ Arguments following the script will be passed to the script args
‣ Remember: put the least possible “business intelligence” into the script

64. Test case: isoforms & proteotypic peptides
‣ Proteotypic peptide: given a list of proteins and cleavage enzyme, a
proteotypic peptide is a peptide that can be produced only by one of those
proteins

65. Test case: isoforms & proteotypic peptides
‣ Proteotypic peptide: given a list of proteins and cleavage enzyme, a
proteotypic peptide is a peptide that can be produced only by one of those
proteins
‣ Customer of the day: “I want to give you one uniprot AC, you print me all the
isoforms in a fasta format and the list list of proteotypic peptide (+ the isoform
they are referring to). Please.”

66. Test case: isoforms & proteotypic peptides
‣ Proteotypic peptide: given a list of proteins and cleavage enzyme, a
proteotypic peptide is a peptide that can be produced only by one of those
proteins
‣ Customer of the day: “I want to give you one uniprot AC, you print me all the
isoforms in a fasta format and the list list of proteotypic peptide (+ the isoform
they are referring to). Please.”
‣ Hopefully enough, you already have a toolkit to build, from a uniprot entry,
a map isoform name -> isoform Protein

67. Test case: isoforms & proteotypic peptides
‣ Proteotypic peptide: given a list of proteins and cleavage enzyme, a
proteotypic peptide is a peptide that can be produced only by one of those
proteins
‣ Customer of the day: “I want to give you one uniprot AC, you print me all the
isoforms in a fasta format and the list list of proteotypic peptide (+ the isoform
they are referring to). Please.”
‣ Hopefully enough, you already have a toolkit to build, from a uniprot entry,
a map isoform name -> isoform Protein
‣ Your turn to play....