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.

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 (Mike Kellen as admin)
Code versioning: Git, hosted on 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)

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

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.

Application Framework: Spring
Test: JUnit as test framework, Easy Mock 3.0 for mock objects in unit tests
Mock Objects: Use Mockito to Mock up objects for tests.
Dates:
- All dates should be in ISO-8601 format.
- ISO-8601 is the default for the joda-time library
- Use the DateTime object from joda-time. Do not use java.text.DateFormat or java.text.SimpleDateFormat.
- The reason for doing this is to make the right thing (ISO-8601) the easy thing. If you instead write out your own date formats, date/timezone bugs are easier to create.

R

R Installation
Bioconductor
Eclipse Plugin for R
- Getting Started Guide for R Eclipse Plugin
You'll also need to install some tools that R package builds depend upon:
- Windows
  1. R Tools
  2. If you have Cygwin installed, do NOT install the Cygwin DLLs (the installer has more detailed instructions)
  3. Install MikTeX
- Mac OSX
  1. Install XCodeso that you have a C compiler
    - Be sure to select installation option "UNIX Development Support"
    - If you install from the "App Store" and are not presented with this option, the following is a work-around:
      - After installing Xcode, go to XCode>Preferences...
      - Go to Downloads > Command Line Tools > Install
      - Follow the prompts to register as an Apple Developer and download the tools.
  2. Install MacTex

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

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

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

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]

Example: empty two level dictionary, add values to it

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

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'
    }

Example: create a populated two-level dictionary

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

Example: empty array, add values to it

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

Example: create a populated array

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

MySQL

MySQL Windows installation instructions
MySQL Workbench - GUI tool for interacting with the MySQL database

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

Firebug http://getfirebug.com/
Fiddler http://www.fiddler2.com/fiddler2/

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/

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