-
Notifications
You must be signed in to change notification settings - Fork 8
/
Config.groovy
284 lines (240 loc) · 10.7 KB
/
Config.groovy
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
import grails.util.Environment
import org.codehaus.groovy.grails.commons.GrailsApplication
/**
* Application Configuration
*
* @author Jeroen Wesbeek
* @since 20100520
*
* Revision information:
* $Rev$
* $Author$
* $Date$
*/
// locations to search for config files that get merged into the main config
// config files can either be Java properties files or ConfigSlurper scripts
//
grails.config.locations = [
// The default configuration properties
"classpath:default.properties",
// The default configuration properties for run-app mode
"file:${basedir}/grails-app/conf/default.properties",
// The external configuration to override the default
"file:${userHome}/.${appName}/${Environment.getCurrent().getName()}.groovy",
// DEPRECATED
//"file:${userHome}/.${appName}/${Environment.getCurrent().getName()}.properties",
"file:${userHome}/.grails/${appName}-${Environment.getCurrent().getName()}-config.groovy"
]
grails.config.locations.each { println "Reading configuration from ${it}" }
grails.mime.file.extensions = true // enables the parsing of file extensions from URLs into the request format
grails.mime.use.accept.header = false
grails.mime.types = [
html: ['text/html', 'application/xhtml+xml'],
xml: ['text/xml', 'application/xml'],
text: 'text/plain',
js: 'text/javascript',
rss: 'application/rss+xml',
atom: 'application/atom+xml',
css: 'text/css',
csv: 'text/csv',
all: '*/*',
json: ['application/json', 'text/json'],
form: 'application/x-www-form-urlencoded',
multipartForm: 'multipart/form-data'
]
// The default codec used to encode data with ${}
grails.views.default.codec = "none" // none, html, base64
grails.views.gsp.encoding = "UTF-8"
grails.converters.encoding = "UTF-8"
// enabled native2ascii conversion of i18n properties files
grails.enable.native2ascii = true
log4j = {
String logFile = "${userHome}/.grails/logs/${appName}_${Environment.getCurrent().getName()}_stacktrace.log"
println "Logging to: ${logFile}"
appenders {
console name:'stdout', layout:pattern(conversionPattern: '%d{yyyy-MM-dd/HH:mm:ss.SSS} %x %-5p %c{2} - %m%n')
rollingFile name:'stacktrace', file:logFile, maxFileSize:"10MB", maxBackupIndex: 10, append:true, layout:pattern(conversionPattern: '%d{yyyy-MM-dd/HH:mm:ss.SSS} %x %-5p %c{2} - %m%n')
}
root {
info 'stacktrace','stdout'
error()
additivity = true
}
error 'org.codehaus.groovy.grails.web.servlet', // controllers
'org.codehaus.groovy.grails.web.pages', // GSP
'org.codehaus.groovy.grails.web.sitemesh', // layouts
'org.codehaus.groovy.grails.web.mapping.filter', // URL mapping
'org.codehaus.groovy.grails.web.mapping', // URL mapping
'org.codehaus.groovy.grails.commons', // core / classloading
'org.codehaus.groovy.grails.plugins', // plugins
'org.codehaus.groovy.grails.orm.hibernate', // hibernate integration
'org.springframework',
'org.hibernate',
'net.sf.ehcache.hibernate'
warn 'org.codehaus.groovy.grails.orm.hibernate',
'org.hibernate' // hibernate integration
error 'grails.app.services.org.grails.plugin.resource',
'grails.app.taglib.org.grails.plugin.resource'
// error 'org.grails.plugin.resource',
// 'grails.app.resourceMappers.org.grails.plugin.resource'
// all 'grails.app', 'dbnp.query', 'dbnp.importer', 'org.dbxp.matriximporter', 'org.dbxp.sam', "dbnp.modules"
warn 'grails.app', 'dbnp.query', 'dbnp.importer', 'org.dbxp.matriximporter', 'org.dbxp.sam', "dbnp.modules"
}
graphviz {
// graphviz installation path is dependent on OS
// (requirement for class diagram plugin)
switch (System.properties["os.name"]) {
case "Mac OS X":
// define mac path to Graphviz dot executable
// (install using macports: sudo port install graphviz)
dot.executable = "/opt/local/bin/dot"
break
default:
// assume the linux default path
dot.executable = "/usr/bin/dot"
}
}
// jquery plugin
grails.views.javascript.library = "jquery"
// Needed for the Spring Security Core plugin:
grails.plugin.springsecurity.userLookup.userDomainClassName = 'dbnp.authentication.SecUser'
grails.plugin.springsecurity.userLookup.authorityJoinClassName = 'dbnp.authentication.SecUserSecRole'
grails.plugin.springsecurity.authority.className = 'dbnp.authentication.SecRole'
grails.plugin.springsecurity.password.algorithm = 'SHA-256'
grails.plugin.springsecurity.password.hash.iterations = 1
grails.plugin.springsecurity.password.encodeHashAsBase64 = true
grails.plugin.springsecurity.dao.reflectionSaltSourceProperty = 'username' // Use the persons username as salt for encryption
grails.plugin.springsecurity.successHandler.targetUrlParameter = 'spring-security-redirect'
// Security is defined below. By default, users that have
// been logged in are allowed access to all controllers and
// other users are denied access. As this is the default,
// we specify the 'open' urls as well as the administrator
grails.plugin.springsecurity.rejectIfNoRule = true
grails.plugin.springsecurity.fii.rejectPublicInvocations = false
grails.plugin.springsecurity.securityConfigType = grails.plugin.springsecurity.SecurityConfigType.InterceptUrlMap
grails.plugin.springsecurity.interceptUrlMap = [
'/*': ['permitAll'],
'/home/gotoStudy/*': ['IS_AUTHENTICATED_REMEMBERED'],
'/home/**': ['permitAll'],
'/study/**': ['permitAll'],
'/publication/list': ['permitAll'],
'/login/**': ['permitAll'],
'/logout/**': ['permitAll'],
'/downloads/**': ['permitAll'],
'/error/**': ['permitAll'],
'/assets/**': ['permitAll'],
'/**/js/**': ['permitAll'],
'/**/css/**': ['permitAll'],
'/**/images/**': ['permitAll'],
'/**/favicon.ico': ['permitAll'],
// Registration and confirming new accounts
'/register/forgotPassword': ['permitAll'],
'/register/resetPassword': ['permitAll'],
'/userRegistration/add': ['permitAll'],
'/userRegistration/sendUserConfirmation': ['permitAll'],
'/userRegistration/confirmUser': ['permitAll'],
// Design view of a public studies
'/studyEditDesign/eventGroupDetails/*': ['permitAll'],
'/studyEditDesign/subjectGroupDetails/*': ['permitAll'],
'/studyEditDesign/dataTableSubjectSelection/*': ['permitAll'],
// View of assay list for public assays
'/measurements/*/assay/list': ['permitAll'],
'/measurements/*/assay/datatables_list': ['permitAll'],
// View of measurements of a public assay
'/measurements/*/assay/show/*': ['permitAll'],
'/measurements/*/assay/showByToken/*': ['permitAll'],
// Rest controllers have their own authentication
'/rest/**': ['permitAll'],
'/measurements/*/rest/**': ['permitAll'],
// API authentication is only accessible for specific users
'/api/authenticate/**': ['ROLE_ADMIN', 'ROLE_CLIENT'],
'/api/**': ['permitAll'],
// Template editor is only accessible for specific users
'/template/**': ['ROLE_ADMIN', 'ROLE_TEMPLATEADMIN'],
// Configuration by administrators
'/assayModule/**': ['ROLE_ADMIN'],
'/setup/**': ['ROLE_ADMIN'],
'/info/**': ['ROLE_ADMIN'],
'/user/**': ['ROLE_ADMIN', 'isFullyAuthenticated()'],
'/userRegistration/confirmAdmin': ['ROLE_ADMIN', 'isFullyAuthenticated()'],
// All other urls are allowed for logged in users
'/**': ['IS_AUTHENTICATED_REMEMBERED'],
]
//Login errors
grails.plugin.springsecurity.errors.login.expired= 'Sorry, your account has expired.'
grails.plugin.springsecurity.errors.login.passwordExpired='Sorry, your password has expired.'
grails.plugin.springsecurity.errors.login.disabled='Sorry, your account is disabled.'
grails.plugin.springsecurity.errors.login.locked='Sorry, your account is locked.'
grails.plugin.springsecurity.errors.login.fail='Sorry, we were not able to find a user with that username and password.'
grails.plugin.springsecurity.denied.message='Sorry, you\'re not authorized to view this page.'
// Spring Security configuration
grails.plugin.springsecurity.useBasicAuth = true
grails.plugin.springsecurity.basic.realmName = "Authentication Required"
grails.plugin.springsecurity.useSessionFixationPrevention = true
grails.plugin.springsecurity.filterChain.chainMap = [
'/rest/hello': 'JOINED_FILTERS,-exceptionTranslationFilter',
'/api/authenticate': 'JOINED_FILTERS,-exceptionTranslationFilter',
'/**': 'JOINED_FILTERS,-basicAuthenticationFilter,-basicExceptionTranslationFilter'
]
// default application properties
application.title = "Phenotype Database"
grails.resources.modules = {
overrides {
'jquery-theme' {
resource id:'theme', url:'https://ajax.googleapis.com/ajax/libs/jqueryui/1.10.3/themes/cupertino/jquery-ui.min.css'
}
}
}
// SAM Configuration
// Fuzzy matching configuration
fuzzyMatching.threshold = [
'default': 0.2,
'featureImporter' : [
'feature': 0.4
],
'measurementImporter': [
'feature' : 0.4,
'sample' : 0.2,
'timepoint' : 0.2,
'subject' : 0.2
]
]
// Example email server configurations, to be put in external configuration file
// (production.groovy or development.groovy)
// Example gmail configuration
/*
grails {
mail {
host = "smtp.gmail.com"
port = 465
username = "<your_address>@gmail.com"
password = "<your_password>"
props = [
"mail.smtp.auth": "true",
"mail.smtp.socketFactory.port": "465",
"mail.smtp.socketFactory.class": "javax.net.ssl.SSLSocketFactory",
"mail.smtp.socketFactory.fallback": "false",
"mail.smtp.starttls.enable": "true"
]
}
}
*/
// Example configuration for mail server without authentication
/*
grails {
mail {
"default" {
from = "<from_address>@example.com"
}
host = "127.0.0.1"
port = 25
props = [:]
}
}
*/
// Alternatively, the configuration can be put in the external production.properties or
// development.properties:
/*
#grails.mail.host=127.0.0.1
#grails.mail.port=2525
*/