installation issue

[Jaeyeon Kihm]

hello,

I tried to install TriSano® Community Edition following the
installation instruction(https://wiki.csinitiative.com/display/tri/
Installation+Instructions) but I've a problem.

- I installed Ubuntu 10.04LTS
- install java6 jdk, jre
- install ruby 4.2, rubygems 1.3.5
- install libxml2, libxml2-dev, libxslt, libxslt-dev
- install postgresql-server-dev 8.4, postgresql-client 8.4, postgresql-
contrib-8.3
- just following the command on instruction.

It was going well, but when I create db I got this message,

/////////////////////
postgres@jaeyeon-laptop:/home/jaeyeon/Downloads/06-18-2010-1237AM/
distro$ ./create_db.sh --trace
(in /home/jaeyeon/Downloads/06-18-2010-1237AM/distro)
no such file to load -- cucumber/rake/task
Creating TriSano database ...
psql: could not connect to server: Connection refused
Is the server running on host "localhost" and accepting
TCP/IP connections on port 5433?
could not connect to server: Connection refused
Is the server running on host "localhost" and accepting
TCP/IP connections on port 5433?
Failed creating database structure for TriSano.
rake aborted!
failed to create database

(See full trace by running task with --trace)
///////////////////////////

I don't know what I could solve this problem.

-Jaeyeon

[Patrick Logan]

Hi Jaeyeon,

I believe this message could be due to using jruby 1.4. The activerecord interface changed from 1.3. Could you try installing with jruby 1.3.1 and let us know whether that makes a difference?

Thanks,
Patrick

"Jaeyeon Kihm" <nex...@gmail.com> wrote:

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[mherrick66]

Hi Jaeyeon,

I installed the JRuby that comes with the downloadable .tar (1.3.1)
and just installed Postgres 8.4 on the same version of Ubuntu you are
on.

It looks like we have a couple of small issues that can be fixed with
updating the config.yml file. I included a fix that works for me below
(postgres port change and priv_uname/password changes0. We'll get the
downloadable .tar file fixed up tomorrow.

postgres_dir: /usr/bin # Location of Postgres client
host: localhost # PostgreSQL host server
port: 5432 # PostgreSQL TCP listen port
environment: production # the name of the environment - corresponds to
rails configuration
basicauth: false # whether HTTP basic auth should be on
database: trisano # Database name
priv_uname: trisano_admin # Database privileged username (used for
upgrade db script)
priv_passwd: admin # Privileged user's password (used for upgrade db
script)
trisano_uname: trisano_user # trisano application username (used by
package app script)
trisano_user_passwd: user # trisano application user password (used by
package app script)
min_runtimes: 2 # minimum number of trisano runtimes
max_runtimes: 5 # maximum number of trisano runtimes
runtime_timeout: 5 # number of seconds that web app thread should wait
before generating HTTP 503 and informing user to try again
dump_file_name: apr29.dump_obfu.attsback # assumes dump file is in
the ./dump directory - example
trisano_production-09-25-2008-1123AM.dump
source_url: # the URL of the TriSano source code. Derivative works
must set this per AGPL.
support_url: # the URL of the TriSano support page.
feedback_email: # the email for TriSano feedback
feedback_url: # the URL of the TriSano feedback page.
default_admin_uid: trisano_admin # the initial user that has admin
privileges

Mike

> >For more options, visit this group athttp://groups.google.com/group/trisano-user?hl=en.

[Joshua Tolley]

PostgreSQL's psql client application gives you this message when it fails to
connect to a server. The installation scripts use psql to create databases,
and apparently failed to find a responding PostgreSQL instance running on
localhost:5433. Is your PostgreSQL server listening, and on that address? Note
that the default port for PostgreSQL is 5432, not 5433, so perhaps you should
change config.yml to use port 5432 instead.

--
Joshua Tolley / eggyknap
End Point Corporation
http://www.endpoint.com

[Jaeyeon Kihm]

Thanks. I build the database successfully. The problem was the default port. It was 5433 but needed to replace to 5432. Additionally, just in case, I also needed to run the shell code with 'postgres' user, and fix the priv_uname is "trisano_admin" and priv_passwd is "admin" on config.yml since I followed below on the installation instruction;

$ sudo su postgres
[sudo] password for $uname:
$ createuser trisano_admin -P
Enter password: admin
Shall the new role be a superuser? (y/n) y


CREATE ROLE

Thanks for help all of you.

-Jaeyeon

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--
Master of Science in Computer Science
Georgia Institute of Technology
Atlanta, GA 30332

1-404-664-8201

[Mike Herrick]

Jaeyeon,

Our apologies, we found a couple other issues:

1. site_config.yml (add "auth_srv_env"), before was getting no UID error from browser:

production:

  inherit: base

  auth_src_env: TRISANO_UID

3. export RAILS_ENV=production 

* add to start_trisano.sh - otherwise was starting in dev mode and not working per instructions

We are going to fix this up in the download tomorrow.

Mike

[Jaeyeon Kihm]

hello,

I finished all instructions well but I got the message below when I tried to run application. Do you guys have any idea about this?

-----------------------------------------
$ ./start_trisano.sh
=> Booting WEBrick
=> Rails 2.3.5 application starting on http://0.0.0.0:3000
./script/../config/../vendor/rails/railties/lib/rails/gem_dependency.rb:119:Warning: Gem::Dependency#version_requirements is deprecated and will be removed on or after August 2010.  Use #requirement
/home/jaeyeon/Downloads/06-18-2010-1237AM/webapp/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_specification.rb:62:in `establish_connection': development database is not configured (ActiveRecord::AdapterNotSpecified)
    from /home/jaeyeon/Downloads/06-18-2010-1237AM/webapp/vendor/rails/activerecord/lib/active_record/connection_adapters/abstract/connection_specification.rb:55:in `establish_connection'
    from script/../config/../vendor/rails/railties/lib/initializer.rb:438:in `initialize_database'
    from script/../config/../vendor/rails/railties/lib/initializer.rb:141:in `process'
    from script/../config/../vendor/rails/railties/lib/initializer.rb:113:in `run'
    from /home/jaeyeon/Downloads/06-18-2010-1237AM/webapp/config/environment.rb:13
    from /home/jaeyeon/Downloads/06-18-2010-1237AM/webapp/config/environment.rb:31:in `require'
    from /home/jaeyeon/Downloads/06-18-2010-1237AM/webapp/../lib/jruby/jruby-1.3.1/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `require'
    from /home/jaeyeon/Downloads/06-18-2010-1237AM/webapp/vendor/rails/activesupport/lib/active_support/dependencies.rb:156:in `require'
    from /home/jaeyeon/Downloads/06-18-2010-1237AM/webapp/vendor/rails/activesupport/lib/active_support/dependencies.rb:521:in `new_constants_in'
    from /home/jaeyeon/Downloads/06-18-2010-1237AM/webapp/vendor/rails/activesupport/lib/active_support/dependencies.rb:156:in `require'
    from /home/jaeyeon/Downloads/06-18-2010-1237AM/webapp/vendor/rails/railties/lib/commands/server.rb:84
    from /home/jaeyeon/Downloads/06-18-2010-1237AM/webapp/vendor/rails/railties/lib/commands/server.rb:31:in `require'
    from /home/jaeyeon/Downloads/06-18-2010-1237AM/webapp/../lib/jruby/jruby-1.3.1/lib/ruby/site_ruby/1.8/rubygems/custom_require.rb:31:in `require'
    from script/server:3

-Jaeyeon

[Mike Herrick]

Number 3 on my list should address that one.

"Jaeyeon Kihm" <nex...@gmail.com> wrote:

>>> trisano-user...@googlegroups.com<trisano-user%2Bunsu...@googlegroups.com>

>>> .
>>> > >For more options, visit this group at
>>> http://groups.google.com/group/trisano-user?hl=en.
>>> > >
>>> >
>>> > --
>>> > Sent from my Android phone with K-9 Mail. Please excuse my brevity.
>>> >
>>> > --
>>> > You received this message because you are subscribed to the Google
>>> Groups "trisano-user" group.
>>> > To post to this group, send email to trisan...@googlegroups.com.
>>> > To unsubscribe from this group, send email to

>>> trisano-user...@googlegroups.com<trisano-user%2Bunsu...@googlegroups.com>

>> trisano-user...@googlegroups.com<trisano-user%2Bunsu...@googlegroups.com>

>> .
>> For more options, visit this group at
>> http://groups.google.com/group/trisano-user?hl=en.
>>
>
>
>
>--
>Master of Science in Computer Science
>Georgia Institute of Technology
>Atlanta, GA 30332
>
>1-404-664-8201
>

[Mike Herrick]

Try making your start_trisano.sh look like this if it does not already.

#!/bin/bash

# Copyright (C) 2007, 2008, 2009, 2010 The Collaborative Software Foundation

#

# This file is part of TriSano.

#

# TriSano is free software: you can redistribute it and/or modify it under the 

# terms of the GNU Affero General Public License as published by the 

# Free Software Foundation, either version 3 of the License, 

# or (at your option) any later version.

#

# TriSano is distributed in the hope that it will be useful, but 

# WITHOUT ANY WARRANTY; without even the implied warranty of 

# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the 

# GNU Affero General Public License for more details.

#

# You should have received a copy of the GNU Affero General Public License 

# along with TriSano. If not, see http://www.gnu.org/licenses/agpl-3.0.txt.

# Starts TriSano - simple config - not intended for production use.

. setenv.sh

export TRISANO_UID=trisano_admin

# MJH added 20-JUN-2010

export RAILS_ENV=production

cd ../webapp

touch ./log/production.log

jruby script/server

[Patrick Logan]

Hi Jaeyeon - are you up and running now?

Patrick Logan
TriSano Development Manager
Collaborative Software Initiative, Inc.
pat...@csinitiative.com
Mobile: 503-476-5387
Skype: patrickdlogan
http://www.csinitiative.com
http://www.trisano.org

[Jaeyeon Kihm]

Hi Patrick,

Yes, the program is running well but I'm currently learning how to use the tool.
My goal is to classify bunch of chief complaints to few labels and analyze the trend of them. I thought I could track the trend of diseases using TriSano but I couldn't find the proper way so currently I'm stuck.
I saw the Dr. David Jackson but seems not enough for me. If you have another user manual or know how to analyze the diseases using CC list please let me know.

Thanks for your consideration.

Sincerely,
Jaeyeon Kihm

[Patrick Logan]

Hi Jaeyeon,

You can read through the documentation on the TriSano community wiki. In
particular you might begin with these two sections on reporting/analysis and
integration.

https://wiki.csinitiative.com/display/tri/Analysis%2C+Visualization%2C+and+Reporting

https://wiki.csinitiative.com/display/tri/Integration

Can you tell us more about your objectives? You would like to apply data
collected with TriSano to some classification engines?

Thanks
-Patrick

[Jaeyeon Kihm]

Hi,

What I'm doing might be quite simple.
I want to analyze the trend of disease using a list of chief complaints of patients such as;

DATE,GENDER,PATIENT_ID,AGE,SYNDROME
"4-16-2009","F","23686","45","RASH ON BODY"
"4-16-2009","F","13840","35","CANT URINATE"
"4-16-2009","M","12895","30","BLURRED VISION"
"4-16-2009","M","18375","33","UNABLE TO VOID"
"4-16-2009","M","2237","44","SOB WEAKNESS"

My idea is classify the syndrome to labels comprised of ICD-9 codes such as Gastrointestinal, Constitutional, Respiratory, Rash, Hemorrhagic, Botulinic, Neurological, and others. We could analyze the trend of 8 clustered syndromes and visualize them easier and more comfortable than visualize each of syndromes.
What I'm going to focus on is mortality rates, temporal patterns of the onset, and peak and recovery of the disease.

At first, I really need the classification tool at least and it might be even better the tool provides any statistic result from the data.

Thanks,
Jaeyeon Kihm

[Patrick Logan]

That sounds interesting, Jaeyeon. TriSano's analysis capabilities are
provided by Pentaho on Postgresql DB (tranformed from the core app's
Postgresql DB). Pentaho has general purpose OLAP and ad hoc querying.
Pentaho sponsors the Weka java-based classification/clustering library. Weka
should be able to connect to the TriSano datawarehouse model fairly easily
through jdbc.

http://www.cs.waikato.ac.nz/ml/weka/

The flow would be essentially:

1. Data collection using TriSano core app.
2. ETL (through our provided script) from the core DB to the TriSano AVR DB.
3. Extract and prepare data from the AVR DB.
4. Use weka workbench