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Standard Tools

These are the tools we have pretty much settled on as a team.  For ease and consistency of development please try to remain on these tools and discuss with the team before introducing competing technologies.

Profilers

Code Coverage

We have been approved for free licenses to use Clover (Atlassian Code Coverage tool) for Eclipse. To install the Clover plug-in for eclipse you can use the update site http://update.atlassian.com/eclipse/clover

Eclipse users: Within Eclipse, select from the menu "Window > Preferences" and click on "Clover > License" and paste the above license string into the license text area.

MONqrDkXrjMnJciwRtLBAEGFOmnBGjNmbRRWECCaUafBQo
mi2Kehqg3mIlkHdhHlTejumx2KzaGJQIsBkyJf66uTXT7W
NPQQsvpRQnqmPnrRpQPSunQNrOQnnRqMNovXXwssmXtvsW
vSttxsuurRqopnmomUUnovrnuoummmmmUUnovrnuoummmm
mUUJXdbW2flkbqtlohpUUnmmmm

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.

R

Python

How to install Python modules

To install easy_install, install the python2.7 version of it from here http://pypi.python.org/pypi/setuptools#files

  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:

    ~/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

    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

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

  3. Example: create a populated dictionary

    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

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

  5. Example: empty array, add values to it

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

  6. Example: create a populated array

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

MySQL

Git

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

Moving files and directories

Git is pretty smart about moving files and directories.  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

Have a large blob of JSON?  Want to see it in human readable format?  Toss it into this web ui: http://jsonformatter.curiousconcept.com/

Web Trace Tools

UML Tools

Class Diagrams

UMLet 11.2 is a "Free UML Tool for Fast UML Diagrams" http://www.umlet.com/

Sequence Diagram Editors

Don’t waste your time with drawing programs when you can just write something similar to psuedocode.

Lucene Search

Browse lucene indices with Luke http://www.getopt.org/luke/