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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.
- 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 admins)
- Code versioning: Subversion, hosted by Atlassian as part of our Jira Studio subscription
- 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
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Eclipse users:
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Within
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Eclipse,
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select
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from
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the
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menu
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"Window
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>
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Preferences"
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and
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click
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on
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"Clover
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>
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License"
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and
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paste
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the
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above
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license
...
string
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into
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the
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license
...
text
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area.
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MONqrDkXrjMnJciwRtLBAEGFOmnBGjNmbRRWECCaUafBQo
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mi2Kehqg3mIlkHdhHlTejumx2KzaGJQIsBkyJf66uTXT7W
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NPQQsvpRQnqmPnrRpQPSunQNrOQnnRqMNovXXwssmXtvsW
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vSttxsuurRqopnmomUUnovrnuoummmmmUUnovrnuoummmm
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mUUJXdbW2flkbqtlohpUUnmmmm
Java
Libraries
At this point we don't
...
have
...
any
...
strict
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licensing
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requirements,
...
however
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to
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maintain
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flexibility
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we
...
have
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to
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be
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careful
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about
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licenses
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for
...
software
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we
...
choose
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to
...
incorporate
...
into
...
our
...
system.
...
The best licenses are open source licenses without copy-left
...
provisions
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(e.g.
...
...
...
) 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
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to
...
use
...
GPL
...
ourselves)
...
if
...
we
...
chose
...
to
...
redistribute
...
the
...
code
...
base
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at
...
a
...
later
...
date.
...
For
...
now,
...
we
...
should
...
just
...
be
...
aware
...
of
...
the
...
mix
...
of
...
licenses
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incorporated
...
into
...
our
...
projects,
...
and
...
have
...
a
...
bias
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for
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open
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source,
...
non-copy
...
left
...
licenses.
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- Application
...
- Framework:
...
- Spring
- Test: JUnit as test framework, Easy Mock 3.0 for mock objects in unit tests
R
Python
Python Examples for Perl programmers
- 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]
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- Example:
...
- create
...
- a
...
- populated
...
- dictionary
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Code Block
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CSV_TO_PRIMARY_FIELDS = { 'name': 'name', 'description': 'description', 'Investigator': 'creator', 'Creation Date': 'creationDate', 'Status': 'status', 'date_released': 'releaseDate', 'version':'version' }
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- Example:
...
- empty
...
- array,
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- add
...
- values
...
- to
...
- it
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Code Block
...
stringAnnotations = [] stringAnnotations.append("foo")
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- Example:
...
- create
...
- a
...
- populated
...
- array
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Code Block
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CSV_SKIP_FIELDS = ["db_id","user_agreement_file_path", "readme_file_path"];
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Subversion
For general SVN info see the SVN book
Moving files and directories
The eclipse plugin for svn generally does a decent job moving files and directories. See also http://svnbook.red-bean.com/en/1.1/re18.html
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Here
...
is
...
an
...
example:
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- You
...
- can
...
- see
...
- that
...
- there
...
- is
...
- a
...
- "deleted"
...
- file
...
- here
...
- but
...
- it
...
- was
...
- actually
...
- "svn
...
- moved"
...
...
- Old
...
- filename
...
...
- New
...
- filename
...
...
- You
...
- can
...
- see
...
- that
...
- the
...
- full
...
- svn
...
- history
...
- is
...
- shown
...
- on
...
- each
...
- page.
...
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
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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
- SVN branch documentation http://svnbook.red-bean.com/en/1.1/ch04s02.html#svn-ch-4-sect-2.1
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- svnmerge.py
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- Documentation
...
...
...
- the
svn switchcommand is handy to change the branch for your local checked out copy of code
How to Set Up Merge Tracking
- Download svnmerge.py
- 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
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- 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
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- 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
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- 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
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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.
- Ensure the branch is working and committed to SVN.
- To see what branches are available for importing, use this command from the branch distribution:
Code Block python svnmerge.py avail
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- One of the results should be '/PLFM/trunk'.
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- import
...
- the
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- changes
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- from
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- trunk
...
- into
...
- the
...
- branch:
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Code Block
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python svnmerge.py merge -S /PLFM/trunk
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- Resolve conflicts,
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- compile,
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- test
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- and
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- commit
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- EVERYTHING
...
- in
...
- the
...
- branch.
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Merge
...
from
...
your
...
branch
...
to
...
trunk
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- Go
...
- to
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- an
...
- up-to-date
...
- local
...
- distribution
...
- of
...
- trunk.
...
- From
...
- the
...
- trunk
...
- distribution
...
- use
...
- the
...
- 'avail'
...
- command
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- (above)
...
- to
...
- find
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- the
...
- branch
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- of
...
- interest.
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- Use
...
- the
...
- following
...
- command
...
- to
...
- find
...
- the
...
- revision(s)
...
- of
...
- interest:
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Code Block
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python svnmerge.py avail -S <your branch>
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- Import the changes from the branch into trunk:
- For all changes
Code Block python svnmerge.py merge -S <your branch>
- For all changes
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- For particular changes
Code Block python svnmerge.py merge -r <your revisions comma separated> -S <your branch>
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- Resolve conflicts,
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- compile,
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- test
...
- and
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- commit.
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Elastic
...
Bamboo
...
We
...
currently
...
have
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MySQL
...
running
...
on
...
our
...
Elastic
...
Bamboo
...
host
...
for
...
the
...
purposes
...
of
...
integration
...
testing.
...
This
...
is
...
accomplished
...
by
...
the
...
...
shell
...
script
...
which
...
is
...
run
...
at
...
boot
...
time
...
for
...
the
...
hosts.
...
If
...
you
...
want
...
to
...
import
...
a
...
database
...
dump,
...
install
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Crowd,
...
etc.,
...
here
...
is
...
how
...
to
...
modify
...
that
...
script:
...
- Log
...
- onto
...
- the
...
- currently
...
- running
...
- elastic
...
- instance
...
- (or
...
- spawn
...
- one
...
- if
...
- none
...
- are
...
- running).
...
...
- Note
...
- that
...
- the
...
- ssh
...
- key
...
- is
...
- on
...
belltown:/work/platform/PasswordsAndCredentials/AtlassianAccountAWSCredentials/elasticbamboo.pk
...
- Note that if you want to log onto the AWS console, Mike's
...
- username
...
- and
...
- password
...
- is
...
- on
...
belltown:/work/platform/PasswordsAndCredentials/AtlassianAccountAWSCredentials/Mike'sPassword
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- From
...
- the
...
- shell
...
- try
...
- out
...
- the
...
- commands
...
- you
...
- want
...
- to
...
- run
...
- at
...
- boot
...
- time
...
- Run
...
- you
...
- build
...
- and
...
- make
...
- sure
...
- it
...
- works
...
- Check
...
- your
...
- changes
...
- to
...
- customize-extras.sh
...
- into
...
- source
...
- control
...
...
- On the bamboo host, overwrite
/mnt/bamboo-ebs/bin/customise-extras.sh
...
- with
...
- your
...
- updated
...
- script.
...
- Follow
...
- these
...
- instructions
...
- to
...
- create
...
- snapshot
...
- and
...
- configure
...
- bamboo
...
- to
...
- use
...
- it
...
...
...
...
- snapshot
- Shutdown the host, and kick off a new build. This should start a new bamboo host that will run your updated script.
- Make sure the build passes!
For more information, see:
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...
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/
...
...
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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