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  • Operating System: what ever floats your boat.
  • IDE: Eclipse commonly used and free
  • Wiki / Issue Tracker / Code Browsing and Reviewing / Automated Builds: we have a Jira Studio subscription  (Nicole Deflaux and Mike Kellen as adminsadmin)
  • Code versioning: SubversionGit, hosted by Atlassian as part of our Jira Studio subscriptionon GitHub.
  • Build System: Maven
  • Build repository manager: see Sage's hosted Artifactory service see jFrog website for info (John Hill and Mike Kellen as admins)

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vSttxsuurRqopnmomUUnovrnuoummmmmUUnovrnuoummmm
mUUJXdbW2flkbqtlohpUUnmmmm

You can also use Jacoco for code coverage. For more information, see Jacoco Code Coverage.

Java

Libraries

At this point we don't have any strict licensing requirements, however to maintain flexibility we have to be careful about licenses for software we choose to incorporate into our system.  The best licenses are open source licenses without copy-left provisions (e.g. Apache License) that give us maximal flexibility in what we later do with the code base.  Some strong copy-left licenses (e.g. GPL) would impose licensing requirements on us (e.g. force us to use GPL ourselves) if we chose to redistribute the code base at a later date. For now, we should just be aware of the mix of licenses incorporated into our projects, and have a bias for open source, non-copy left licenses.

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Python

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  1. Make sure you are running the right version of easy_install http://superuser.com/questions/256717/easy-install-the-wrong-version-of-python-modules-mac-os

  2. From the shell:

    Code Block
    
~/platform/trunk>easy_install progressbar
Searching for progressbar
Reading http://pypi.python.org/simple/progressbar/
Reading http://code.google.com/p/python-progressbar/
Reading http://code.google.com/p/python-progressbar
Best match: progressbar 2.3
Downloading http://python-progressbar.googlecode.com/files/progressbar-2.3.tar.gz
Processing progressbar-2.3.tar.gz
Running progressbar-2.3/setup.py -q bdist_egg --dist-dir /var/folders/h0/h0pR5063FtCMCzzo1bt2WU+++TI/-Tmp-/easy_install-a29dGI/progressbar-2.3/egg-dist-tmp-3Dwzuw
zip_safe flag not set; analyzing archive contents...
Adding progressbar 2.3 to easy-install.pth file

Installed /Library/Python/2.7/site-packages/progressbar-2.3-py2.7.egg
Processing dependencies for progressbar
Finished processing dependencies for progressbar


Python Examples for Perl programmers

  1. Example: empty dictionary, add values to it

    Code Block
    
layer = {}
layer["type"] = row[1]
layer["status"] = row[2]
layer["name"] = row[3]
layer["numSamples"] = row[4]
layer["platform"] = row[5]
layer["version"] = row[6]
layer["qcBy"] = row[11]


  2. Example: empty two level dictionary, add values to it

    Code Block
    
layer = {}
layer['foo'] = {}
layer['foo']['bar'] = 3
layer['hello'] = {}
layer['hello']['world'] = 42


  3. Example: create a populated dictionary

    Code Block
    
CSV_TO_PRIMARY_FIELDS = {
    'name': 'name',
    'description': 'description',
    'Investigator': 'creator',
    'Creation Date': 'creationDate',
    'Status': 'status',
    'date_released': 'releaseDate',
    'version':'version'
    }


  4. Example: create a populated two-level dictionary

    Code Block
    
MY_FAKE_LAYER = {'foo': {'bar': 3}, 'hello': {'world': 42}}


  5. Example: empty array, add values to it

    Code Block
    
stringAnnotations = []
    stringAnnotations.append("foo")


  6. Example: create a populated array

    Code Block
    
CSV_SKIP_FIELDS = ["db_id","user_agreement_file_path", "readme_file_path"];


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Git

For general SVN info see the SVN bookGit info see the Git page.  Or maybe you're interested in our Git Workflow instead.

Moving files and directories

The eclipse plugin for svn generally does a decent job Git is pretty smart about moving files and directories. See also http://svnbook.red-bean.com/en/1.1/re18.html

Here is an example:

svn gets really upset though when you do more complicated things like created a file, delete that file, then make a directory with the same name in the same location as the deleted file. (but that is a pretty odd thing to do anyway)

When in doubt, make a developer branch and try it there first.http://svnbook.red-bean.com/en/1.1/ch04s02.html#svn-ch-4-sect-2.1

Developer branches

Want to make a drastic change and run it by the team before merging it to trunk? Want to check in broken code? Make a branch and do it there.

Resources

How to Set Up Merge Tracking

  1. Download svnmerge.py
  2. Make a branch directory for yourself (you'll only need to do this once)
    Code Block
    
svn mkdir https://sagebionetworks.jira.com/svn/PLFM/branches/deflaux
  3. Make a new branch from trunk
    Code Block
    
svn copy https://sagebionetworks.jira.com/svn/PLFM/trunk https://sagebionetworks.jira.com/svn/PLFM/branches/deflaux/automatedIntegrationTesting
  4. Have both trunk and your new branch on your local hard drive, this assumes you already have trunk checked out in directory ~/platform
    Code Block
    
cd ~/platform
svn update trunk
svn checkout https://sagebionetworks.jira.com/svn/PLFM/branches/deflaux/automatedIntegrationTesting
  5. Initialize merge tracking
    Code Block
    
cd trunk
svnmerge.py init ../automatedIntegrationTesting
svn commit -F svnmerge-commit-message.txt
cd ../automatedIntegrationTesting
svnmerge.py init ../trunk
svn commit -F svnmerge-commit-message.txt

Alternative: Initialize merge tracking and switch to your new branch

Code Block

cd trunk
svnmerge.py init https://sagebionetworks.jira.com/svn/PLFM/branches/deflaux/sts
svn commit -F svnmerge-commit-message.txt
svn switch https://sagebionetworks.jira.com/svn/PLFM/branches/deflaux/sts
svnmerge.py init https://sagebionetworks.jira.com/svn/PLFM/trunk
svn commit -F svnmerge-commit-message.txt

How to merge

Merge from trunk to your branch

Best Practice: merge changes from trunk to your branch every morning Monday through Friday. This reduces the pain later when you want to merge from your branch to trunk.

  1. Ensure the branch is working and committed to SVN.
  2. To see what changes and/or branches are available for importing, use this command from the branch distribution:
    Code Block
    
python svnmerge.py avail -l
    • Windows Users: One of the results should be '/PLFM/trunk'.
  3. import the changes from trunk into the branch:
    • to merge all changes
      Code Block
      
python svnmerge.py merge -S /PLFM/trunk
    • to merge one or more particular changes
      Code Block
      
python svnmerge.py merge -r #,#,# -S /PLFM/trunk
  4. Resolve conflicts, compile, test and commit EVERYTHING in the branch.
    Code Block
    
svn ci -F svnmerge-commit-message.txt

Merge from your branch to trunk

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Code Block

python svnmerge.py avail -S <your branch>

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  1. For all changes
    Code Block
    
python svnmerge.py merge -S <your branch>
  2. For particular changes
    Code Block
    
python svnmerge.py merge -r <your revisions comma separated> -S <your branch>

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 It can even detect that you've renamed a file without you having to tell it so explicitly.  Basically, you shouldn't have problems.  If you do, write about the solution you found here.

Developer branches

Bottom line.  They're easy in git, so USE THEM!  For more info see the Git page for resources.

Tools To Know About

Pretty-Print JSON

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