...
| Table of Contents |
|---|
Developer AWS Accounts
Use your individual AWS account under the Sage consolidated bill for AWS experiments. The rule of thumb is that if you cannot shut off what ever you are running while you are on vacation, it belongs in the Production AWS Account.
Production AWS Account
Use your IAM Account for:
- S3
- EC2
- Elastic MapReduce (command line access only right now)
- You will need to log into the AWS console with you IAM login and password: https://325565585839.signin.aws.amazon.com/console/ec2
...
Use
...
the
...
platform@sagebase.org
...
Account
...
for:
...
- Elastic
...
- Beanstalk
...
- console
...
- usage
...
- of
...
- Elastic
...
- MapReduce
...
- You
...
- will
...
- need
...
- to
...
- log
...
- into
...
- the
...
- AWS
...
- console
...
- with
...
- the
...
- platform@sagebase.org
...
- username
...
- and
...
- password:
...
...
Credentials,
...
passwords,
...
ssh
...
keys
...
You
...
can
...
find
...
them
...
on
...
our
...
shared
...
servers.
...
When
...
storing
...
passwords
...
locally
...
on
...
your
...
laptop
...
(which
...
already
...
has
...
an
...
encrypted
...
drive,
...
yay
...
!)
...
you
...
might
...
also
...
consider
...
using
...
...
...
.
| Code Block |
|---|
/work/platform/PlatformIAMCreds>hostname
fremont
/work/platform/PlatformIAMCreds>ls -la
ndeflaux@fremont:/work/platform/PlatformIAMCreds> ls -la
total 56
drwxrwx--- 2 ndeflaux FHCRC\platform 4096 2011-03-05 15:32 .
drwxrwxr-x 7 platform FHCRC\platform 4096 2011-03-05 15:32 ..
-r--r----- 1 ndeflaux FHCRC\platform 126 2011-03-04 12:35 brian.holt_creds.txt
-r--r----- 1 ndeflaux FHCRC\platform 126 2011-03-04 12:35 bruce.hoff_creds.txt
-r--r----- 1 ndeflaux FHCRC\platform 129 2011-03-04 12:35 david.burdick_creds.txt
-r--r----- 1 ndeflaux FHCRC\platform 125 2011-03-04 12:35 john.hill_creds.txt
-r--r----- 1 ndeflaux FHCRC\platform 127 2011-03-04 12:35 mike.kellen_creds.txt
-r--r----- 1 ndeflaux FHCRC\platform 130 2011-03-04 12:35 nicole.deflaux_creds.txt
-rw-r----- 1 ndeflaux FHCRC\platform 236 2011-03-04 12:35 passwords.txt
-r--r----- 1 ndeflaux FHCRC\platform 332 2011-03-04 12:35 platform_cred.txt
-rw-r----- 1 ndeflaux FHCRC\platform 1697 2011-03-04 12:35 PlatformKeyPairEast.pem
-r--r----- 1 ndeflaux FHCRC\platform 1693 2011-03-04 12:35 PlatformKeyPair.pem
-r--r----- 1 ndeflaux FHCRC\platform 134 2011-03-04 12:35 repository.service_creds.txt
-r--r----- 1 ndeflaux FHCRC\platform 120 2011-03-04 12:35 test_creds.txt
{code}
h3. First time accessing the console
Use your IAM credentials (which can be found in {{ |
First time accessing the console
Use your IAM credentials (which can be found in fremont:/work/platform/PlatformIAMCreds
...
)
...
to
...
create
...
a
...
password
...
for
...
yourself
...
using
...
the
...
IAM
...
tools.
...
You
...
can
...
install
...
the
...
IAM
...
tools
...
on
...
your
...
machine
...
http://docs.amazonwebservices.com/IAM/latest/GettingStartedGuide/index.html?GetTools.html
...
or
...
use
...
them
...
on
...
fremont.
...
| Code Block |
|---|
ssh you@fremont
cd /work/platform
export AWS_IAM_HOME=/work/platform/bin/IAMCli-1.1.0
export AWS_CREDENTIAL_FILE=/work/platform/PlatformIAMCreds/YourFirstname.YourLastname_cred.txt
export PATH=$PATH:$AWS_IAM_HOME/bin
iam-useraddloginprofile -u YourFirstname.YourLastname -p aDecentPassword
{code}
h2. How To
h3. Figure out if AWS is broken
AWS occasionally has issues. To figure out whether the problem you are currently experiencing is their fault or not:
# Check the AWS status console to see if they are reporting any problems [ |
How To
Figure out if AWS is broken
AWS occasionally has issues. To figure out whether the problem you are currently experiencing is their fault or not:
- Check the AWS status console to see if they are reporting any problems http://status.aws.amazon.com/
...
- Check
...
- the
...
- most
...
- recent
...
- messages
...
- on
...
- the
...
- forums
...
...
- Problems
...
- often
...
- get
...
- reported
...
- there
...
- first.
...
- If
...
- you
...
- still
...
- do
...
- not
...
- find
...
- evidence
...
- that
...
- the
...
- problem
...
- is
...
- AWS's
...
- fault,
...
- search
...
- the
...
- forums
...
- for
...
- your
...
- particular
...
- issue.
...
- Its
...
- likely
...
- that
...
- someone
...
- else
...
- has
...
- run
...
- into
...
- the
...
- same
...
- exact
...
- problem
...
- in
...
- the
...
- past.
...
- Still
...
- no
...
- luck?
...
- Ask
...
- your
...
- coworkers
...
- and/or
...
- post
...
- a
...
- question
...
- to
...
- the
...
- forums.
...
Run
...
a
...
Report
...
to
...
Know
...
Who
...
has
...
Accessed
...
What
...
When
...
Use
...
Elastic
...
MapReduce
...
to
...
run
...
a
...
script
...
on
...
all
...
our
...
logs
...
in
...
the
...
bucket
...
logs.sagebase.org
...
.
...
There
...
are
...
some
...
scripts
...
in
...
bucket
...
emr.sagebase.org/scripts
...
that
...
will
...
do
...
the
...
trick.
...
If
...
you
...
want
...
to
...
change
...
what
...
they
...
do,
...
feel
...
free
...
to
...
make
...
new
...
scripts
...
.
Here is what a configured job looks like:
And here is some sample output from the job. Note that:
- All Sage employees will have their sagebase.org username as their IAM username
- Platform users register with an email address and we will use that email address as their IAM username.
- User
d9df08ac799f2859d42a588b415111314cf66d0ffd072195f33b921db966b440is the platform@sagebase.org user (also known as Brian Holt :-). In general, you should only see activity from that user when we are using BucketExplorer to manage our files in S3.Code Block arn:aws:iam::325565585839:user/nicole.deflaux [18/Feb/2011:19:32:44 +0000] REST.GET.OBJECT human_liver_cohort/readme.txt arn:aws:iam::325565585839:user/nicole.deflaux [18/Feb/2011:19:32:56 +0000] REST.GET.OBJECT human_liver_cohort/readme.txt arn:aws:iam::325565585839:user/nicole.deflaux [18/Feb/2011:19:32:58 +0000] REST.GET.OBJECT human_liver_cohort/readme.txt arn:aws:iam::325565585839:user/nicole.deflaux [18/Feb/2011:17:47:45 +0000] REST.GET.LOCATION - arn:aws:iam::325565585839:user/nicole.deflaux [18/Feb/2011:23:42:17 +0000] REST.GET.LOGGING_STATUS - arn:aws:iam::325565585839:user/nicole.deflaux [18/Feb/2011:23:42:19 +0000] REST.HEAD.OBJECT human_liver_cohort.tar.gz arn:aws:iam::325565585839:user/nicole.deflaux [18/Feb/2011:19:32:40 +0000] REST.GET.BUCKET - arn:aws:iam::325565585839:user/nicole.deflaux [18/Feb/2011:17:47:46 +0000] REST.GET.BUCKET - arn:aws:iam::325565585839:user/nicole.deflaux [17/Feb/2011:01:48:42 +0000] REST.GET.BUCKET - arn:aws:iam::325565585839:user/nicole.deflaux [17/Feb/2011:01:48:42 +0000] REST.GET.LOCATION - arn:aws:iam::325565585839:user/nicole.deflaux [17/Feb/2011:01:48:51 +0000] REST.HEAD.OBJECT mouse_model_of_sexually_dimorphic_atherosclerotic_traits.tar.gz arn:aws:iam::325565585839:user/nicole.deflaux [17/Feb/2011:01:48:51 +0000] REST.GET.ACL mouse_model_of_sexually_dimorphic_atherosclerotic_traits.tar.gz arn:aws:iam::325565585839:user/nicole.deflaux [18/Feb/2011:23:42:17 +0000] REST.GET.ACL - arn:aws:iam::325565585839:user/nicole.deflaux [18/Feb/2011:23:42:19 +0000] REST.GET.ACL human_liver_cohort.tar.gz arn:aws:iam::325565585839:user/nicole.deflaux [18/Feb/2011:23:42:57 +0000] REST.HEAD.OBJECT mouse_model_of_sexually_dimorphic_atherosclerotic_traits.tar.gz arn:aws:iam::325565585839:user/nicole.deflaux [18/Feb/2011:23:42:17 +0000] REST.GET.NOTIFICATION - arn:aws:iam::325565585839:user/nicole.deflaux [18/Feb/2011:23:42:57 +0000] REST.GET.ACL mouse_model_of_sexually_dimorphic_atherosclerotic_traits.tar.gz arn:aws:iam::325565585839:user/test [17/Feb/2011:01:55:44 +0000] REST.GET.OBJECT mouse_model_of_sexually_dimorphic_atherosclerotic_traits.tar.gz arn:aws:iam::325565585839:user/test [16/Feb/2011:23:13:42 +0000] REST.GET.OBJECT human_liver_cohort/readme.txt arn:aws:iam::325565585839:user/test [16/Feb/2011:23:22:02 +0000] REST.GET.OBJECT human_liver_cohort/expression/expression.txt d9df08ac799f2859d42a588b415111314cf66d0ffd072195f33b921db966b440 [16/Feb/2011:23:06:17 +0000] REST.HEAD.OBJECT human_liver_cohort/readme.txt d9df08ac799f2859d42a588b415111314cf66d0ffd072195f33b921db966b440 [16/Feb/2011:22:28:38 +0000] REST.GET.ACL - d9df08ac799f2859d42a588b415111314cf66d0ffd072195f33b921db966b440 [16/Feb/2011:22:39:57 +0000] REST.GET.LOCATION - d9df08ac799f2859d42a588b415111314cf66d0ffd072195f33b921db966b440 [16/Feb/2011:22:40:09 +0000] REST.COPY.OBJECT bxh_apoe/causality_result/causality_result_adipose_male.txt d9df08ac799f2859d42a588b415111314cf66d0ffd072195f33b921db966b440 [16/Feb/2011:22:40:16 +0000] REST.HEAD.OBJECT bxh_apoe/causality_result/causality_result_adipose_male.txt . . . Downloads per file: bxh_apoe/networks/BxH-ApoE_Brain_Male_batch_3_14_coexp-network.txt 2 bxh_apoe/networks/muscle_male-nodes.txt 2 bxh_apoe/networks/BxH-ApoE_Liver_Male_batch_3_4_coexp-log.txt 2 bxh_apoe/networks/SCN10_BxH-ApoE_Adipose_Male_batch_3_10_coexp.sif 2 bxh_apoe/networks/SCN19_muscle_female_bayesian.sif 2 human_liver_cohort/networks/deLiver_liver_all_adjusted_DE-Octave8_coexp-nodes.txt 2 bxh_apoe/networks/BxH-ApoE_Liver_Male_batch_3_4_coexp-annotation.txt 2 bxh_apoe/networks/BxH-ApoE_Brain_Male_batch_3_14_coexp-nodes.txt 2 bxh_apoe/networks/muscle_female-nodes.txt 2 human_liver_cohort/networks/QuickChip_female_bayesian-annotation.txt 2 . . . bxh_apoe/networks/liver_female_coexp-annotation.txt 2 bxh_apoe/networks/SCN15_BxH-ApoE_Muscle_Female_batch_1_11_coexp.sif 2 bxh_apoe/networks/SCN7_brain_female_bayesian.sif 2 human_liver_cohort/sage_bionetworks_user_agreement.pdf 5 bxh_apoe/phenotype/ 1 bxh_apoe/networks/SCN14_BxH-ApoE_Liver_Male_batch_3_4_coexp.sif 2 Downloads per user: arn:aws:iam::325565585839:user/nicole.deflaux 17 arn:aws:iam::325565585839:user/test 3 d9df08ac799f2859d42a588b415111314cf66d0ffd072195f33b921db966b440 931
...
Upload a dataset to S3
For the initial upload, a GUI tool called BucketExplorer (http://www.bucketexplorer.com/
...
)
...
is
...
used.
...
 Uploads are
...
done
...
from
...
the
...
internal
...
host
...
fremont.fhcrc.org
...
using
...
the
...
local
...
access
...
account
...
'platform',
...
with
...
the
...
same
...
password
...
as
...
the
...
platform@sagebase.org
...
account.
...
The
...
most
...
efficient
...
way
...
to
...
connect
...
is
...
to
...
use
...
an
...
NX
...
protocol
...
client
...
(
...
http://www.nomachine.com/download.php
...
)
...
to
...
get
...
a
...
virtual
...
desktop
...
as
...
the
...
user
...
platform.
...
Once
...
connected
...
the
...
preconfigured
...
BucketExplorer
...
can
...
be
...
found
...
in
...
the
...
application
...
menu
...
in
...
the
...
lower
...
left
...
corner
...
of
...
the
...
screen.
...
Mac
...
OSX
...
Users
...
I
...
installed
...
"NX
...
Client
...
for
...
Mac
...
OSX"
...
but
...
it
...
complained
...
that
...
I
...
was
...
missing
...
bin/nxssh
...
and
...
bin/nxservice
...
.
...
That
...
stuff
...
was
...
not
...
installed
...
under
...
Applications
...
but
...
instead
...
under
...
/Users/deflaux/usr/NX/
...
The
...
initial
...
datasets
...
are
...
stored
...
in
...
/work/platform/.
...
This
...
entire
...
collection
...
is
...
mirrored
...
exactly
...
and
...
can
...
transfered
...
by
...
dragging
...
and
...
dropping
...
into
...
the
...
data01.sagebase.org
...
s3
...
bucket.
...
This
...
operation
...
should
...
be
...
done
...
as
...
user
...
platform,
...
as
...
all
...
files
...
should
...
be
...
readable
...
by
...
said
...
user
...
to
...
facilitate
...
the
...
transfer.
...
BucketExplorer
...
is
...
very
...
efficient,
...
and
...
will
...
do
...
hash
...
comparisons
...
and
...
only
...
transfer
...
what
...
files
...
have
...
changed.
...
One
...
can
...
also
...
get
...
a
...
visual
...
comparison
...
of
...
what
...
files
...
have
...
changed
...
using
...
the
...
'Comparer'
...
button.
...
During
...
the
...
transfer,
...
the
...
program
...
will
...
parallelize
...
the
...
transfer
...
into
...
20
...
streams
...
for
...
very efficient use of outgoing bandwidth to the cloud.
Create a new IAM group
You can install the IAM tools on your machine http://docs.amazonwebservices.com/IAM/latest/GettingStartedGuide/index.html?GetTools.html
...
or
...
use
...
them
...
on
...
fremont.
...
We
...
are
...
storing
...
our
...
access
...
policies
...
in
...
SVN:
...
http://sagebionetworks.jira.com/source/browse/PLFM/trunk/configuration/awsIamPolicies
...
See the IAM documentation for more details about how to do this but here is an example of how one of our existing groups was created:
| Code Block |
|---|
ssh you@fremont
cd /work/platform
export AWS_IAM_HOME=/work/platform/bin/IAMCli-1.1.0
export AWS_CREDENTIAL_FILE=/work/platform/PlatformIAMCreds/YourFirstname.YourLastname_cred.txt
export PATH=$PATH:$AWS_IAM_HOME/bin
iam-groupcreate -g ReadOnlyUnrestrictedDataUsers
iam-groupuploadpolicy -g ReadOnlyUnrestrictedDataUsers -p ReadOnlyUnrestrictedDataPolicy -f /work/platform/awsIamPolicies/ReadOnlyUnrestrictedDataPolicy.txt
iam-groupadduser -u test -g ReadOnlyUnrestrictedDataUsers
iam-grouplistusers -g ReadOnlyUnrestrictedDataUsers
{code}
h3. Create a new user and add them to IAM groups
You can install the IAM tools on your machine [ |
Create a new user and add them to IAM groups
You can install the IAM tools on your machine http://docs.amazonwebservices.com/IAM/latest/GettingStartedGuide/index.html?GetTools.html
...
or
...
use
...
them
...
on
...
fremont.
...
Note
...
that
...
this
...
is
...
for
...
adding
...
Sage
...
employees
...
to
...
groups
...
by
...
hand.
...
The
...
repository
...
service
...
will
...
take
...
care
...
of
...
adding
...
Web
...
Client
...
and
...
R
...
Client
...
users
...
to
...
the
...
right
...
IAM
...
group(s)
...
after
...
they
...
sign
...
a
...
EULA
...
for
...
a
...
dataset.
...
See
...
the
...
IAM
...
documentation
...
for
...
more
...
details
...
about
...
how
...
to
...
do
...
this
...
but
...
here
...
is
...
an
...
example
...
of
...
how
...
Bruce's
...
IAM
...
user
...
was
...
created:
...
| Code Block |
|---|
ssh you@fremont
cd /work/platform
export AWS_IAM_HOME=/work/platform/bin/IAMCli-1.1.0
export AWS_CREDENTIAL_FILE=/work/platform/PlatformIAMCreds/YourFirstname.YourLastname_cred.txt
export PATH=$PATH:$AWS_IAM_HOME/bin
iam-usercreate -u bruce.hoff -g Admins -k -v > PlatformIAMCreds/bruce.hoff_creds.txt
{code}
|
Then
...
give
...
the
...
user
...
their
...
credentials
...
file.
...
How
...
to
...
connect
...
to
...
RDS
...
Use
...
the
...
...
...
.
...
You
...
can
...
install
...
it
...
locally
...
on
...
your
...
machine
...
(do
...
this
...
by
...
installing
...
a
...
local
...
MySQL
...
database
...
too.)
...
Or
...
you
...
can
...
use
...
it
...
on
...
fremont.
...
The
...
firewall
...
currently
...
only
...
allows
...
you
...
to
...
connect
...
from
...
a
...
server
...
inside
...
the
...
Fred
...
Hutch
...
network.
...
If
...
you
...
are
...
working
...
from
...
home,
...
ssh
...
to
...
fremont
...
and
...
then
...
do
...
this.
...
You
...
can
...
find
...
the
...
database
...
password
...
in
...
fremont:/work/platform/PlatformIAMCreds/passwords.txt
...
This
...
is
...
the
...
super
...
user
...
so
...
be
...
careful
...
!
...
| Code Block |
|---|
~>hostname
fremont
~>/usr/bin/mysql -u platform -h repo.c5sxx7pot9i8.us-east-1.rds.amazonaws.com -p
Enter password:
Welcome to the MySQL monitor. Commands end with ; or \g.
Your MySQL connection id is 6212
Server version: 5.5.8-log Source distribution
Copyright (c) 2000, 2010, Oracle and/or its affiliates. All rights reserved.
This software comes with ABSOLUTELY NO WARRANTY. This is free software,
and you are welcome to modify and redistribute it under the GPL v2 license
Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.
mysql> show databases;
+--------------------+
| Database |
+--------------------+
| information_schema |
| innodb |
| mysql |
| performance_schema |
| repositorydb |
+--------------------+
5 rows in set (0.07 sec)
mysql> use repositorydb;
Reading table information for completion of table and column names
You can turn off this feature to get a quicker startup with -A
showDatabase changed
mysql> show tables;
+------------------------+
| Tables_in_repositorydb |
+------------------------+
| GAEJDOANALYSISRESULT |
| GAEJDOANNOTATIONS |
| GAEJDODATASET |
| GAEJDODATASETANALYSIS |
| GAEJDODATEANNOTATION |
| GAEJDODOUBLEANNOTATION |
| GAEJDOINPUTDATALAYER |
| GAEJDOLAYERLOCATION |
| GAEJDOLAYERLOCATIONS |
| GAEJDOLONGANNOTATION |
| GAEJDOPROJECT |
| GAEJDORESOURCEACCESS |
| GAEJDOREVISION |
| GAEJDOSCRIPT |
| GAEJDOSTRINGANNOTATION |
| GAEJDOUSER |
| GAEJDOUSERGROUP |
| NUCLEUS_TABLES |
+------------------------+
18 rows in set (0.08 sec)
mysql> desc GAEJDODATASET;
+---------------------+--------------+------+-----+---------+----------------+
| Field | Type | Null | Key | Default | Extra |
+---------------------+--------------+------+-----+---------+----------------+
| ID | bigint(20) | NO | PRI | NULL | auto_increment |
| ANNOTATIONS_ID_OID | bigint(20) | YES | MUL | NULL | |
| CREATION_DATE | datetime | YES | | NULL | |
| CREATOR | varchar(256) | YES | | NULL | |
| DESCRIPTION | varchar(256) | YES | | NULL | |
| NAME | varchar(256) | YES | | NULL | |
| NEXT_VERSION_ID_OID | bigint(20) | YES | MUL | NULL | |
| RELEASE_DATE | datetime | YES | | NULL | |
| REVISION_ID_OID | bigint(20) | YES | MUL | NULL | |
| STATUS | varchar(256) | YES | | NULL | |
+---------------------+--------------+------+-----+---------+----------------+
10 rows in set (0.07 sec)
mysql> select count(*) from GAEJDODATASET ;
+----------+
| count(*) |
+----------+
| 114 |
+----------+
1 row in set (0.08 sec)
mysql> quit
{code}
h3. How do I bootstrap a local MySQL database?
# Setup MySQL
#* [ |
How do I bootstrap a local MySQL database?
...
...
- Create
...
- your
...
- empty
...
- database
...
Code Block
...
~/>/usr/local/mysql/bin/mysql -u root Welcome to the MySQL monitor. Commands end with ; or \g. Your MySQL connection id is 1910 Server version: 5.5.9 MySQL Community Server (GPL) Copyright (c) 2000, 2010, Oracle and/or its affiliates. All rights reserved. Oracle is a registered trademark of Oracle Corporation and/or its affiliates. Other names may be trademarks of their respective owners. Type 'help;' or '\h' for help. Type '\c' to clear the current input statement. mysql> show databases; +--------------------+ | Database | +--------------------+ | information_schema | | mysql | | performance_schema | | test | +--------------------+ 4 rows in set (0.06 sec) mysql> create database test2; Query OK, 1 row affected (0.00 sec) mysql> show databases; +--------------------+ | Database | +--------------------+ | information_schema | | mysql | | performance_schema | | test | | test2 | +--------------------+ 5 rows in set (0.04 sec)
...
How to load a JDO schema into MySQL
- Use the mysql client to connect to the database host and drop/create the database as needed
- Set up the database configuration
trunk/lib/jdomodels/src/main/resources/datanucleus.propertiesis already configured for a local MySQL instance- For RDS, locally edit
trunk/lib/jdomodels/src/main/resources/datanucleus.properties
...
- to
...
- include
...
- the
...
- RDS
...
- host
...
- ,
...
- user,
...
- and
...
- password
...
- (do
...
- not
...
- check
...
- in
...
- any
...
- production
...
- database
...
- passwords
...
- into
...
- svn)
...
- Run
...
- the
...
- Datanucleus
...
- schema
...
- creation
...
- tool
...
Code Block
...
cd trunk/lib/jdomodels mvn compile mvn datanucleus:enhance mvn datanucleus:schema-create
...
How to load data into an empty repository service
This is a bit of a mess right now, but it does do the trick. Expect this to get better over time. You can use this to load data into a repository service whether it is running on beanstalk or locally on your laptop.
| Code Block |
|---|
>ssh fremont
>cd /work/platform/DatasetMetadataLoader
/work/platform/DatasetMetadataLoader> curl http://charon-vpn-010162.fhcrc.org:8080/repo/v1/dataset
{"results":[],"totalNumberOfResults":0,"paging":{}}
/work/platform/DatasetMetadataLoader> ./datasetCsv2Loader.py TheDatasets2.csv charon-vpn-010162.fhcrc.org:8080 AllDatasetLayerLocations.csv
lot of output here . . .
/work/platform/DatasetMetadataLoader> curl http://charon-vpn-010162.fhcrc.org:8080/repo/v1/dataset?limit=1
{
"results":[
{
"name":"Gastric Cancer ACRG",
"annotations":"/repo/v1/dataset/0/annotations",
"id":"0",
"version":"0.0.1",
"creator":"Asian Cancer Research Group, Inc., (ACRG)",
"description":null,
"creationDate":1299375144172,
"status":"Future",
"uri":"/repo/v1/dataset/0",
"etag":"384011750",
"releaseDate":null,
"layer":"/repo/v1/dataset/0/layer",
"hasExpressionData":false,
"hasGeneticData":false,
"hasClinicalData":false
}
],
"totalNumberOfResults":114,
"paging":{
"next":"/repo/v1/dataset?offset=2&limit=1"
}
}
{code}
h2. Notes for the sake of posterity
h3. Gotchas Getting Started with Beanstalk
Here are some gotchas I ran into when using beanstalk for the first time:
# I created a key pair in US West and was confused when I couldn't get beanstalk to use that key pair.
#* Beanstalk is only in US East so you have to make and use a key pair from US East
#* Get the key pair PlatformKeyPairEast from fremont
# I could not ssh to my box even though I had the right key pair and the hostname.
#* I needed to edit the default firewall setttings to open up port 22
# My serlvet didn't work right away and I wanted to look at stuff on disk.
#* The servlet WAR is expanded under {{ |
Notes for the sake of posterity
Gotchas Getting Started with Beanstalk
Here are some gotchas I ran into when using beanstalk for the first time:
- I created a key pair in US West and was confused when I couldn't get beanstalk to use that key pair.
- Beanstalk is only in US East so you have to make and use a key pair from US East
- Get the key pair PlatformKeyPairEast from fremont
- I could not ssh to my box even though I had the right key pair and the hostname.
- I needed to edit the default firewall setttings to open up port 22
- My serlvet didn't work right away and I wanted to look at stuff on disk.
- The servlet WAR is expanded under
/var/lib/tomcat6/webapps/ROOT/
- The servlet WAR is expanded under
...
- If you want to save time (and a beanstalk deployment) you can overwrite that WAR with a new WAR if you want.
- The log files are here:
Code Block /var/log /var/log/tomcat6/monitor_catalina.log.lck /var/log/tomcat6/tail_catalina.log /var/log/tomcat6/tail_catalina.log.lck /var/log/tomcat6/monitor_catalina.log /var/log/httpd/error_log /var/log/httpd/access_log /var/log/httpd/elasticbeanstalk-access_log /var/log/httpd/elasticbeanstalk-error_log
...
- Error:
...
- java.lang.NoClassDefFoundError:
...
- javax/servlet/jsp/jstl/core/Config
...
- In
...
- a
...
- tomcat
...
- container,
...
- such
...
- as
...
- Elastic
...
- Beanstalk,
...
- you
...
- have
...
- to
...
- include
...
- jstl.jar
...
- manually,
...
- hence
...
- this
...
- entry.
...
Code Block
...
<dependency> <groupId>javax.servlet</groupId> <artifactId>jstl</artifactId> <version>1.2</version> </dependency>
...
- Here's
...
- what
...
- your
...
- deployment
...
- might
...
- look
...
- like
...
- when
...
- things
...
- are
...
- working
...
- well:
