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h1. |
Step
...
by
...
Step
...
Guide
...
to
...
Install
...
caArray
...
2.x
...
Grid
...
Service
...
(caArray
...
2.2
...
and
...
Under)
...
Topic
...
:
...
caArray
...
Installation
...
and
...
Upgrade
...
Release
...
:
...
Up
...
to
...
caArray
...
2.2
...
Date
...
entered
...
:
...
01/26/2009
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Introduction
There are three components installed during caArray's
...
installation
...
process:
...
UPT,
...
caArray
...
and
...
caArray
...
Grid
...
Service
...
(refer
...
to
...
...
...
...
...
...
...
...
...
...
...
...
...
...
...
).
...
UPT
...
is
...
a
...
mandatory
...
application
...
used
...
for
...
caArray's
...
user
...
access
...
control.
...
The
...
caGrid
...
Service
...
is
...
used
...
to
...
advertise
...
your
...
caArray
...
application
...
on
...
the
...
...
...
...
.
...
The
...
caGrid
...
Portal
...
provides
...
a
...
visual
...
display
...
of
...
the
...
services
...
that
...
are
...
running
...
on
...
the
...
caGrid
...
infrastructure
...
and
...
the
...
institutions
...
that
...
are
...
participating
...
in
...
the
...
caBIG
...
program.
...
You
...
can
...
easily
...
find
...
caBIG
...
services,
...
participants,
...
and
...
points
...
of
...
contact
...
on
...
the
...
caGrid
...
Portal.
...
You
...
can
...
also
...
query
...
caGrid
...
data
...
services,
...
share
...
your
...
queries,
...
and
...
search
...
for
...
the
...
queries
...
of
...
other
...
community
...
members.
...
Advertising
...
your
...
caGrid
...
Service
...
on
...
caGrid
...
Portal
...
is
...
optional.
...
You
...
may
...
choose
...
to
...
participate
...
at
...
a
...
later
...
time,
...
or
...
you
...
may
...
choose
...
not
...
to
...
participate
...
at
...
all.
...
The
...
official
...
caGrid
...
Service
...
configuration
...
steps
...
can
...
be
...
found
...
in
...
...
...
...
...
...
.
...
This
...
knowledge
...
base
...
entry
...
offers
...
a
...
supplemental
...
step
...
by
...
step
...
installation
...
guide
...
based
...
on
...
our
...
hands-on
...
experience
...
here
...
at
...
Columbia
...
University.
...
Prerequisite
caArray 2.x
...
application
...
must
...
be
...
running
...
prior
...
to
...
the
...
activation
...
of
...
your
...
caGrid
...
service
...
on
...
the
...
caGrid
...
Portal.
...
However,
...
the
...
grid
...
service
...
is
...
not
...
required
...
for
...
the
...
caArray
...
application
...
to
...
run.
...
Abbreviation
...
Used
...
The
...
following
...
abbreviations
...
will
...
be
...
used
...
through
...
the
...
text:
...
Abbreviation | Comment |
|---|---|
<installation_directory> |
...
The |
...
location |
...
where |
...
you |
...
keep |
...
the |
...
files |
...
downloaded. |
...
|
...
/app_data1/caArray2.1 |
...
|
...
The location where you are going to install caArray and caGrid service. |
...
|
...
The location for the caGrid service files, see step 2 |
Step 1. Make appropriate changes to install.properties file
File Location: <installation_directory>/install.properties
...
This
...
is
...
the
...
step
...
to
...
configure
...
Install.properties
...
file
...
before
...
the
...
deployment
...
of
...
caArray
...
Grid
...
service
...
begins.
...
caGrid
...
service
...
and
...
caArray
...
share
...
the
...
same
...
Install.properties
...
file.
...
It
...
is
...
important
...
to
...
specify
...
following
...
properties:
...
Property | Comments |
|---|---|
application.base.path=/app_data1/caarray_app/caarray |
...
The |
...
location |
...
where |
...
you |
...
are |
...
going |
...
to |
...
install |
...
caArray |
...
(i.e. |
...
the |
...
deployment |
...
of |
...
caGrid |
...
service |
...
and |
...
caArray |
...
application). |
...
|
...
need |
...
to |
...
be |
...
pre-created |
...
before |
...
installation |
...
start. |
...
|
...
: |
...
<application_base_path> |
...
must |
...
be |
...
different |
...
from |
...
|
...
or |
...
the |
...
installation |
...
will |
...
fail. |
...
grid.index |
...
URL |
...
= |
...
...
NCI |
...
caGrid |
...
service's |
...
production |
...
webserver |
...
name |
...
domain.name=afapp1.c2b2.columbia.edu |
...
Our |
...
private |
...
DNS |
...
name |
...
where |
...
the |
...
caArray |
...
is |
...
installed. |
...
grid.static.grid.hostname=localhost |
...
We |
...
use |
...
localhost |
...
here |
...
because |
...
our |
...
caGrid |
...
service |
...
is |
...
on |
...
the |
...
same |
...
machine |
...
as |
...
caArray |
...
(a |
...
default |
...
configuration). |
...
|
...
caGrid |
...
service's |
...
hostname |
...
must |
...
be |
...
used |
...
if |
...
it |
...
is |
...
installed |
...
on |
...
a |
...
different |
...
machine |
...
from |
...
caArray |
...
application. |
...
grid.static.grid.port=80 |
...
Our |
...
publicly |
...
accessible |
...
port |
...
to |
...
DMZ |
...
Zone |
Step 2.
...
Run
...
ant
...
to
...
compile
...
source
...
code
...
File
...
location:
...
<installation_directory>/ant
...
During
...
the
...
compiling
...
process,
...
Java
...
class
...
files
...
will
...
be
...
deployed
...
into
...
following
...
two
...
directories,
...
as
...
defined
...
in
...
Install.properties
...
file:
...
Directory | Comments | |
|---|---|---|
|
...
For caGrid service (created |
...
during |
...
the |
...
deployment) |
...
|
...
For Jboss service (created |
...
during |
...
the |
...
deployment) |
...
Step 3.
...
Make
...
appropriate
...
changes
...
to
...
web.xml
...
file
...
File
...
Location:
...
<grid.home>/server/default/deploy/wsrf.war/WEB-INF/web.xml
| Code Block |
|---|
} <param-name>defaultPort</param-name> <param-value>80</param-value> {code} |
The
...
web.xml
...
file
...
contains
...
the
...
port
...
and
...
protocol
...
your
...
grid
...
service
...
will
...
be
...
advertised
...
as.
...
The
...
port
...
defined
...
here
...
should
...
be
...
the
...
same
...
publicly
...
accessible
...
port
...
as
...
defined
...
in
...
your
...
property
...
file
...
(grid.static.grid.port
...
in
...
Step
...
1
...
).
...
It
...
is
...
port
...
80
...
in
...
our
...
case,
...
as
...
defined
...
in
...
our
...
property
...
file.
...
caArray
...
Application
...
and
...
Port
...
Forwarding
Our caGrid service server physically resides on an internal server (afapp1.c2b2.columbia.edu:18080)
...
behind
...
the
...
firewall.
...
This
...
address,
...
however,
...
is
...
not
...
reachable
...
from
...
outside
...
of
...
Columbia
...
University's
...
network.
...
Our
...
publicly
...
accessible
...
address
...
(a
...
logical
...
hostname)
...
is:
...
http://caarraygrid.c2b2.columbia.edu:80/wsrf/services/cagrid/CaArraySvc
...
Since
...
our
...
caGrid
...
service
...
is
...
actually
...
running
...
on
...
the
...
internal
...
server's
...
port
...
18080,
...
a
...
proxy
...
server
...
will
...
forward
...
any
...
incoming
...
request
...
from
...
the
...
publicly
...
accessible
...
port
...
80
...
to
...
port
...
18080
...
on
...
the
...
internal
...
host.
...
The
...
port
...
used
...
in
...
web.xml
...
should
...
be
...
the
...
port
...
from
...
the
...
publicly
...
accessible
...
address,
...
not
...
the
...
port
...
on
...
the
...
internal
...
server.
...
Step
...
4.
...
Make
...
appropriate
...
changes
...
to
...
server-config.wsdd
...
File
...
Location:
...
<grid.home>/server/default/deploy/wsrf.war/WEB-INF/etc/globus_wsrf_core/server-config.wsdd
...
This
...
is
...
to
...
add
...
your
...
caGrid
...
service's
...
publicly
...
accessible
...
DNS
...
name
...
into
...
configuration
...
file.
| Code Block |
|---|
} <parameter name="logicalHost" value="caarraygrid.c2b2.columbia.edu"/> {code} h2. Step |
Step 5.
...
Make
...
appropriate
...
changes
...
to
...
CaArraySvc_registration.xml
...
File
...
Location:
...
<grid.home>/server/default/deploy/wsrf.war/WEB-INF/etc/cagrid_CaArraySvc/CaArraySvc_registration.xml
...
This
...
file
...
has
...
the
...
URL
...
to
...
the
...
Index
...
Server
...
where
...
you
...
can
...
see
...
if
...
your
...
service
...
is
...
advertised.
...
Make
...
sure
...
it
...
contains
...
following:
| Code Block |
|---|
} <ServiceGroupEPR> <wsa:Address>http://cagrid-index.nci.nih.gov:8080/wsrf/services/DefaultIndexService</wsa:Address> </ServiceGroupEPR> {code} h2. Step |
Step 6.
...
Make
...
appropriate
...
changes
...
to
...
serviceMetadata.xml
...
File
...
Location:
...
<grid.home>/server/default/deploy/wsrf.war/WEB-INF/etc/cagrid_CaArraySvc/serviceMetadata.xml
...
This
...
file
...
contains
...
the
...
contact
...
information
...
for
...
your
...
caGrid
...
service.
...
Your
...
caGrid
...
Service
...
will
...
not
...
be
...
recognized
...
in
...
the
...
caGrid
...
Portal
...
without
...
the
...
proper
...
identification
...
defined
...
here.
...
The
...
following
...
is
...
in
...
the
...
top
...
of
...
the
...
file.
| Code Block |
|---|
} <ns2:pointOfContactCollection> <ns3:PointOfContact affiliation="Columbia University Medical Center" email="my_contact@my.organization" firstName="My FirstName" lastName="My LastName" phoneNumber="My Phone" role="DBA" xmlns:ns3="gme://caGrid.caBIG/1.0/gov.nih.nci.cagrid.metadata.common"/> </ns2:pointOfContactCollection> {code} |
The
...
following
...
is
...
at
...
the
...
bottom
...
of
...
the
...
file.
| Code Block |
|---|
} <ns1:hostingResearchCenter> <ns14:ResearchCenter displayName="Columbia University Medical Center" shortName="CUMC" xmlns:ns14="gme://caGrid.caBIG/1.0/gov.nih.nci.cagrid.metadata.common"> <ns14:Address country="US" locality="New York" postalCode="10032" stateProvince="NY" street1="My Street1." street2=""/> <ns14:pointOfContactCollection> <ns14:PointOfContact affiliation="Columbia University Medical Center" email="my_contact@my.organization" firstName="My FirstName" lastName="My LastName" phoneNumber="My Phone" role="DBA"/> </ns14:pointOfContactCollection> </ns14:ResearchCenter> </ns1:hostingResearchCenter> {code} h2. Step |
Step 7.
...
Restart
...
JBoss
...
server
...
for
...
grid
...
service
| Code Block |
|---|
} cd $\{application.base.path\}/jboss-4.0.4.GA/bin nohup ./run.sh & {code} h2. Step |
Step 8.
...
Testing
...
caGrid
...
Service
...
Installed
...
The
...
table
...
below
...
summarizes
...
four
...
methods
...
we
...
used
...
to
...
test
...
if
...
our
...
newly
...
installed
...
caGrid
...
Service
...
(
...
caarraygrid
...
)
...
works
...
properly:
...
Objects | Procedures | Results |
|---|---|---|
Does caarraygrid Registered in NCI Index? |
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
...
|
...
|
...
Following |
...
Information |
...
should |
...
be |
...
returned:<ns8:Address |
...
xmlns:ns8="http://schemas.xmlsoap.org/ws/2004/03/addressing"> |
...
...
</ns8:Address> |
...
Is |
...
our |
...
registration |
...
accurate |
...
with |
...
ServiceMetaData? |
...
|
...
|
...
|
...
|
...
|
...
...
...
|
...
|
...
It |
...
should |
...
return |
...
our |
...
contact |
...
information, |
...
such |
...
as:<ns1:ServiceMetadata |
...
xmlns:ns1="gme://caGrid.caBIG/1.0/gov.nih.nci.cagrid.metadata"> |
...
|
...
|
...
description="" |
...
name="CaArraySvc" |
...
version="1.1" |
...
|
...
|
...
|
...
affiliation="Columbia |
...
University |
...
Medical |
...
Center" |
...
.... |
...
Is |
...
there |
...
any |
...
data |
...
returned |
...
with |
...
DomainModel? |
...
|
...
|
...
|
...
|
...
|
...
...
|
...
|
...
It |
...
should |
...
return |
...
some |
...
of |
...
our |
...
data |
...
from |
...
caArray, |
...
such |
...
as: |
...
<ns1:DomainModel |
...
projectDescription="Version |
...
2.0 |
...
caArray |
...
Model" |
...
projectLongName="caArray" |
...
|
...
projectVersion="2" |
...
|
...
|
...
|
...
bidirectional="false"> |
...
|
...
|
...
maxCardinality="1" |
...
minCardinality="0" |
...
roleName="annotation"> |
...
|
...
refid="5423786E-6C04-59EA-E044-0003BA3F9857"/> |
...
.... |
...
Can |
...
I |
...
see |
...
my |
...
caGrid |
...
Service |
...
online? |
...
|
...
|
...
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
|
...
Checking |
...
that |
...
caGrid |
...
is online |
Have a comment?
Please leave your comment in the caArray End User Forum.
| Wiki Markup |
|---|
online*
!Check-cagrid-online.JPG|alt="Screenshot showing Checking that caGrid is online"!|
h2. Have a comment?
Please leave your comment in the [caArray End User Forum|https://cabig-kc.nci.nih.gov/Molecular/forums/viewtopic.php?f=6&t=577].
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