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Page History
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Analysis-Server
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Installation
...
Guide
...
This
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page
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provides
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an
...
introduction
...
to
...
Analysis
...
Server,
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with
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installation
...
and
...
troubleshooting
...
information.
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{panel}
h2. Introduction
The Analysis Server performs |||||
|
Introduction
The Analysis Server performs on-the-fly
...
statistical
...
calculations
...
for
...
the
...
caIntegartor
...
application.
...
It
...
can
...
be
...
hosted
...
on
...
the
...
same
...
machine
...
that
...
runs
...
the
...
any
...
application
...
(ex.
...
Rembrandt
...
or
...
ISPY)
...
or
...
it
...
can
...
be
...
run
...
on
...
any
...
number
...
of
...
remote
...
compute
...
machines.
...
In
...
the
...
remote
...
configuration,
...
each
...
compute
...
machine
...
communicates
...
with
...
the
...
appropriate
...
application
...
via
...
the
...
JBossMQ
...
Java
...
Messaging
...
Service
...
(JMS)
...
provided
...
by
...
JBoss.
...
It
...
is
...
important
...
to
...
note
...
that
...
each
...
compute
...
machine
...
does
...
not
...
require
...
its
...
own
...
JBoss
...
instance.
...
The
...
Analysis
...
Server
...
relies
...
on
...
the
...
JMS
...
queues
...
defined
...
in
...
the
...
JBoss
...
instance
...
running
...
the
...
caIntegator
...
application,
...
such
...
as
...
Rembrandt.
...
Analysis-commons
...
is
...
a
...
module
...
which
...
defines
...
classes
...
for
...
communicating
...
with
...
the
...
analysis
...
server.
...
caIntegrator
...
Applications
...
like
...
Rembrandt
...
,
...
I-SPY
...
etc
...
use
...
the
...
request
...
and
...
response
...
classes
...
defined
...
in
...
the
...
analysis
...
commons
...
module
...
for
...
communication
...
with
...
the
...
analysis
...
server.
Requirements
The following assumptions are in place:
You have Java and Ant installed, as listed below
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R and Rserve have been installed. Please see the Rserve homepage at:
http://stats.math.uni-augsburg.de/Rserve/
...
| Multiexcerpt include | ||||||
|---|---|---|---|---|---|---|
|
And the Rserve installation instructions:
http://stats.math.uni-augsburg.de/Rserve/doc.shtml
...
| Multiexcerpt include | ||||||
|---|---|---|---|---|---|---|
|
It is recommended that you read the Rserve installation instructions before installing R. Specifically, the Rserve instructions recommend building the R distribution from source using the (color:red)
...
--enable-R-shlib
...
flag
...
(color).
...
The
...
R
...
source
...
distribution
...
can
...
be
...
obtained
...
from
...
R
...
project
...
site:
...
...
| Multiexcerpt include | ||||||
|---|---|---|---|---|---|---|
|
Setting the Environment Variables:
| Note |
|---|
The purpose of setting operating system environment variables is so that the Java SDK and Ant build tool are available to run from anywhere in the system. |
Linux
To set the environment variables in Linux, follow these steps:
Step | Action |
|---|---|
1 | As the root user, enter the following in the /etc/profile file. |
...
|
...
ANT_HOME= |
...
( |
...
)<installation_directory>( |
...
) |
...
/apache-ant-1.7.0 |
...
|
...
PATH=$JAVA_HOME/bin:$ANT_HOME/bin:$PATH |
...
2 | Log out and log back in so that the system recognizes your changes. |
Verifying the Environment Variables in Linux
To verify that environment variables have been set correctly, follow these steps:
Step | Action |
|---|---|
1 | From the command line, enter: |
2 | To verify your Java SDK installation, enter java -version from a command prompt. |
...
. |
Connection to CVS Repository
1) Connect to CVS repository
2) Here are the parameters
a) Host: cbiocvs2.nci.nih.gov
...
b)
...
Repository
...
path:
...
/share/content/cvsroot
...
c)
...
User:
...
anonymous
...
d)
...
Password:
...
anonymous
...
e)
...
Connection
...
type:
...
pserver
...
Downloading
...
and
...
Deploying
...
the
...
Codebase
...
Step
...
1
...
Check
...
out caintergrator-analysis commons from HEAD or provided CVS tag. Built it using ant script. (Please follow the steps)
a) Open a COMMAND prompt. cd into caintergrator-analysis commons folder.
b) then type ant build_dependency . It will start the build and get the message
BUILD SUCCESSFUL.
c) Do a CVS check out of the caintegrator-analysis-server
Step:2
Download the latest client jar file (use the exceptions version) from:
http://stats.math.uni-augsburg.de/Rserve/down.shtml
...
| Multiexcerpt include | ||||||
|---|---|---|---|---|---|---|
|
Copy the downloaded file into the lib directory under the analysis server install directory and rename it to Rserve.jar .
Step :3
1) Build it using ant script from command prompt.
a) cd into caintergrator-analysis commons folder.
b) then type ant build_tar . It will start the build and you will get the message
BUILD SUCCESSFUL.
Step 4
Setup JMS Configuration Files:
1) Copy the file "caintegrator-jbossmq-destinations-service.xml"
...
from
...
\artifacts
...
to
...
the
...
directory
...
where
...
you
...
installed
...
JBoss.
...
/jboss-4.0.4.GA/server/default/deploy/jms
...
folder
...
2)
...
Copy
...
the
...
application
...
specific
...
file
...
for
...
example
...
"rembrandt-jbossmq-destinations-service.xml"
...
(for
...
REMBRANDT)
...
from
...
\artifacts
...
to
...
the
...
directory
...
where
...
you
...
installed
...
JBoss.
...
/jboss-4.0.4.GA/server/default/deploy/jms
...
folder
Step 5
Deploy the Analysis Server.
| Warning |
|---|
The purpose of setting operating system environment variables is so that the Java SDK and Ant build tool are available to run from anywhere in the system. |
Step 5.1
Copy the caintegrator-analysis-server.tar
...
file
...
created
...
to
...
the
...
directory
...
/local/content/caintegrator
...
.
...
Step
...
5.2
...
Type
...
the
...
command
...
:
...
tar
...
-xvf
...
caintegrator-analysis-server.tar
...
Step 6
Go to the newly created directory /local/content/caintegrator/bin
...
.
...
Type
...
the
...
commands:
...
chmod u+x
...
*.sh
...
dos2unix *.sh
Step 7
Start Rserve by typing:
./startRserve.sh
...
Rserve should now be running. The last line printed on the console should be:
"Rserv started in daemon mode."
Step 8
Go to the directory /home/caintegrator (you can do this by just typing cd).
Start the analysis server by executing the command:
./S92Rserver start
Additional post-deployment test case instructions
1) Open the file/local/content/caintegrator/log/analysisServer.log
...
and
...
you
...
should
...
see
...
something
...
similar
...
to:
...
a)
...
[translationalResearch:main
...
]
...
INFO
...
gov.nih.nci.caintegrator.analysis.server.RThread
...
-
...
Done
...
initializing
...
Rserver
...
connection
...
elapsedTime=5100
...
b)
...
[translationalResearch:main
...
]
...
INFO
...
gov.nih.nci.caintegrator.analysis.server.RThread
...
-
...
RThread
...
name=Thread-0
...
successfully
...
initialized
...
R
...
connection.
...
5046
...
2)
...
There
...
may
...
be
...
a
...
warning:
...
a)
...
[translationalResearch:main
...
]
...
WARN
...
gov.nih.nci.caintegrator.analysis.server.AnalysisServer
...
-
...
could
...
not
...
establish
...
connection
...
with...
...
But
...
this
...
is
...
of
...
no
...
concern.
...
It
...
is
...
because
...
there
...
will
...
be
...
no
...
JMS
...
MQs
...
available
...
until
...
JMS
...
message
...
Queues
...
have
...
been
...
established,
...
running
...
and
...
listed
...
in
...
the
...
JNDI
...
lookup
...
found
...
at
...
the
...
location
...
specified
...
in
...
the
...
property:
...
3)
...
After
...
you
...
deploy
...
the
...
application
...
you
...
should
...
return
...
to
...
this
...
log
...
file
...
and
...
see
...
the
...
following:
...
a)
...
[translationalResearch:main
...
]
...
INFO
...
gov.nih.nci.caintegrator.analysis.server.AnalysisServer
...
-
...
Now
...
listening
...
for
...
requests...
...
Troubleshooting
...
:
...
- "could
...
- not
...
- establish
...
- connection
...
- with
...
- provider.."
...
- when
...
- starting
...
- the
...
- Analysis
...
- Server.
...
This
...
error
...
can
...
occur
...
when
...
the
...
Java
...
Messaging
...
Service
...
(JMS)
...
provider
...
is
...
not
...
running
...
or
...
has
...
not
...
fully
...
initialized.
...
Make
...
sure
...
that
...
the
...
JMS
...
provider
...
that
...
is
...
configured
...
in
...
the
...
analysis
...
server
...
build
...
file
...
is
...
running.
...
If
...
it
...
is
...
running
...
but
...
has
...
not
...
fully
...
initialized
...
the
...
analysis
...
server
...
will
...
automatically
...
connect
...
when
...
it
...
is
...
fully
...
initialized.
...
- Analysis
...
- Server
...
- appears
...
- to
...
- be
...
- running
...
- but
...
- no
...
- results
...
- are
...
- returned.
...
Using
...
the
...
jmx-console
...
(see
...
the
...
JBoss
...
documentation)
...
application
...
go
...
to
...
the
...
jboss.mq.destination
...
section
...
and
...
inspect
...
the
...
AnalysisResponseQueue.
...
Make
...
sure
...
that
...
the
...
receivers
...
count
...
equals
...
1.
...
If
...
it
...
is
...
greater
...
than
...
1
...
then
...
there
...
is
...
another
...
listener
...
on
...
the
...
queue
...
which
...
is
...
stealing
...
the
...
results
...
from
...
application.
...
Next
...
inspect
...
the
...
AnalysisRequestQueue.
...
Make
...
sure
...
that
...
the
...
receivers
...
count
...
is
...
equal
...
to
...
the
...
number
...
of
...
analysis
...
server
...
machines.
...
For
...
example
...
if
...
you
...
have
...
configured
...
four
...
analysis
...
server
...
machines
...
then
...
the
...
receivers
...
count
...
should
...
equal
...
four.
...
If
...
the
...
receiver
...
counts
...
are
...
not
...
as
...
expected
...
then
...
the
...
problem
...
may
...
stem
...
from
...
network/firewall
...
issues
...
or
...
from
...
a
...
conflicting
...
instance
...
of
...
the
...
application.
...
- If
...
- you
...
- are
...
- using
...
- a
...
- version
...
- of
...
- JBoss
...
- other
...
- than
...
- 4.0.2,
...
- you
...
- should
...
- replace
...
- the
...
- following
...
- jar
...
- files:
...
concurrent.jar
...
jbossmq-client.jar
...
jboss-common-client.jar
...
jboss-system-client.jar
...
jnp-client.jar
...
in
...
the
...
lib
...
directory
...
under
...
the
...
analysis
...
server
...
install
...
directory,
...
with
...
the
...
corresponding
...
jar
...
files
...
from the JBoss distribution.
Steps to add a Data File
Step 1
The caIntegrator-ODI GForge project files page has data files for particular application
For example:
Rembrandt:
Rembrandt_mas5.dataMatrix_275_10-15-07.Rda
...
Rembrandt_UnifiedGene.dataMatrix_275_10-15-07.Rda
...
Ispy:
...
newDataFile.zip
...
Step
...
2
...
Copy
...
the
...
data
...
file
...
to
...
the
...
directory
...
local/content/caintegrator/Rdatafiles/
...
Step
...
3
...
Restart
...
the
...
analysis
...
server
...
Log
...
in
...
to
...
the
...
analysis
...
machine
...
Stop
...
the
...
analysis
...
server
...
by
...
executing
...
the
...
command
...
:
./S92Rserver
...
stop
Start the analysis server by executing the command:
./S92Rserver start
Using the Analysis Server for Development Purposes:
On caIntegrator project, for development, the developers share a common analysis server and have a dedicate JMS node for their local Jboss.
This allows us to independently develop and test queries against the analysis server.
You can setup something similar for development using our files
1) Copy StartStopNodes_develop to /home/caIntegrator and started and stopped similar to S92Rserver
./StartStopNodes_develop stop
And
./StartStopNodes_develop start
2) Copy runDeveloperNodes.sh to /local/content/caintegrator/bin/
...
And
...
modify
...
it
...
by
...
adding
...
a
...
new
...
line
...
for
...
each
...
developer
...
using
...
this
...
file
...
as
...
an
...
example
...
3)
...
Copy
...
and rename
...
analysisServerDeveloper1.properties
...
to
...
local/content/caintegrator/bin/
...
And
...
modify
...
the
...
ip
...
address
...
of
...
the
...
developer
...
in
...
this
...
file
...
plus
...
the
...
file
...
name
...
should
...
match
...
the
...
setting
...
in
...
the
...
runDeveloperNodes.sh
...
file
...
Next
...
use
...
localhost:1099
...
on
...
your
...
server
...
to
...
connect
...
to
...
the
...
analysis
...
server.
...
You
...
do
...
not
...
need
...
to
...
start
...
and
...
stop
...
the
...
analysis
...
server
...
for
...
each
...
developer
...
unless
...
your
...
going
...
to
...
upload
...
a
...
new
...
R-binary
...
file.
...
You
...
can
...
substitute
...
actual
...
developer
...
name
...
to
...
identify
...
each
...
node.
