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nectar_web.conf
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# rename this file to nectar::webv2.yml and put a ':' after 'name' if
# you want to use YAML like in old versions of Catalyst
name NECTAR
default_view TT ## if more than one View, set default (o/w, $c->view makes a random view)
#For RSS
format RSS 2.0
author Sungsam Gong (aka. Sung Gong, sung@bio.cc)
description Next Generation Cardiovascular TrAnslational Research
copyright Copyright: (C) 2012 Sungsam Gong
lang en-gb
time_zone GMT
rss_generator Sungsam Gong with the help of Catalyst::View::XML::Feed
logo http://samul.org/static/images/garland_logo.png
# A hash to map real variant callers and those in DBIx::Class way
diBayes DiBaye
GATKs Gatk
SmallIndels SmallIndel
Samtools Samtool
CGA Cgvar
# For json service (see Controller/Util/Service.pm)
gene hgnc
patient bru_code
patient_gene hgnc
disease diag_code
target target_name
run run_name
disease_keyword disease
# this is for auto completion
# see lib/Nectar/Web2/Controller/Util/Service.pm for details
# see root/src/Site/sub_search.tt2
model_gene NECTAR::DistinctGene
model_patient CARDIODB::MetaPatient
model_patient_gene CARDIODB::MetaPatientGene
model_disease CARDIODB::MetaDisease
model_target CARDIODB::MetaTarget
model_run CARDIODB::Run
model_disease_keyword UNIPROT::DistinctDisease
#File Uploading (https://metacpan.org/module/Catalyst::Request::Upload)
#uploadtmp /data/tmp/Nectar (use default /tmp)
# paging
page 1
limit 10
#For Email
admin_to NECTAR admin <sung.gong@yahoo.com>
admin_cc Sung Gong <gong.sungsam@gmail.com>
#Cache (memcached)
cache_for 500
# lib/Nectar/Agent/EnsemblRest.pm
ens_rest http://grch37.rest.ensembl.org
#JSON
#<View::JSON>
# allow_callback 1
# callback_param nectar
# expose_stash json # defaults to everything
# encoding en_gb
#</View::JSON>
#BASESPACE API
redirect_uri https://cardiodb.org/nectar/vcf
grant_type authorization_code
client_id f51e778c417d478caeab6264459d136e
client_secret b47d2e8675074fc79e270c84d515e65a
#http://www.catalystframework.org/calendar/2010/3
#http://wiki.catalystframework.org/wiki/cachingdbicqueries
<Plugin::Cache>
<backend>
namespace NectarMutation:
class Cache::Memcached
server 127.0.0.1:11211
</backend>
</Plugin::Cache>
# http://search.cpan.org/dist/Catalyst-Plugin-AutoCRUD/lib/Catalyst/Plugin/AutoCRUD.pm#SITES_CONFIGURATION
# URL/schema
<Plugin::AutoCRUD>
basepath about/schema/autocrud
tt_path /data/Serve/Web/Cardiodb.org/Nectar-WebV3.00/root/src/Schema/
tt_path /data/Serve/Web/Cardiodb.org/Nectar-WebV3.00/root/src/Schema/full-fat
tt_path /data/Serve/Web/Cardiodb.org/Nectar-WebV3.00/root/src/Schema/skinny
<sites>
<default>
<cardiodb>
delete_allowed no
create_allowed no
update_allowed no
</cardiodb>
</default>
</sites>
</Plugin::AutoCRUD>
# Model
host localhost
database CARDIODB_DEVEL
user nectar # this user is to call stored procedure (get_alignment_by_fam)within the controller (lib/Nectar/Web/Controller/Browser/Mutation.pm)
passwd snrnsk
<Model::CARDIODB>
schema_class Nectar::Schema::CARDIODB
#traits QueryLog::AdoptPlack
#for caching with memcached
traits Caching
<connect_info>
dsn dbi:mysql:database=CARDIODB_DEVEL;host=localhost
user nectar
password snrnsk
AutoCommit 1
cursor_class DBIx::Class::Cursor::Cached
</connect_info>
</Model::CARDIODB>
<Model::UNIPROT>
schema_class Nectar::Schema::UNIPROT
#traits QueryLog::AdoptPlack
#for caching with memcached
traits Caching
<connect_info>
dsn dbi:mysql:database=UNIPROT;host=localhost
user nectar
password snrnsk
AutoCommit 1
cursor_class DBIx::Class::Cursor::Cached
</connect_info>
</Model::UNIPROT>
<Model::NECTAR>
schema_class Nectar::Schema::NECTAR
<connect_info>
dsn dbi:mysql:database=NECTAR;host=localhost
user nectar # should write on NECTAR (or NECTAR_DEVEL)
password snrnsk
#AutoCommit 1
#cursor_class DBIx::Class::Cursor::Cached
</connect_info>
</Model::NECTAR>
<Model::COSMIC>
schema_class Nectar::Schema::COSMIC
<connect_info>
dsn dbi:mysql:database=COSMIC;host=localhost
user nectar
password snrnsk
#AutoCommit 1
#cursor_class DBIx::Class::Cursor::Cached
</connect_info>
</Model::COSMIC>
#Authentication
#https://metacpan.org/module/Catalyst::Plugin::Authentication#CONFIGURATION
<Plugin::Authentication>
default_realm members
<members> # a default realm
use_session 1
<credential>
class Password
password_field password
#password_type clear #plain-text
password_type self_check #SHA-1 key
</credential>
<store>
class DBIx::Class #Catalyst::Authentication::Store::DBIx::Class
user_model NECTAR::User #required
# https://metacpan.org/module/Catalyst::Authentication::Store::DBIx::Class#CONFIGURATION
role_column roles
</store>
</members>
</Plugin::Authentication>