/*
 * Edited and managed by the WP1 for eTRIKS tranSMART deployment
 * NOTE
 * ----
 * This configuration assumes that the development environment will be used with
 * run-app and the production environment will be used with the application
 * packaged as a WAR and deployed to tomcat. Running grails run-war or otherwise
 * running a WAR with the development profile set up or activating the
 * production environment when running grails run-app are scenarios that have
 * NOT been tested.
 */

// eTRIKS tranSMART conf file 11-2016

// Core variables
def catalinaBase      = System.getProperty('catalina.base') ?: '.'
def explodedWarDir    = catalinaBase + '/webapps/transmart'
def solrPort          = 8983
def searchIndex       = catalinaBase + '/searchIndex'
def jobsDirectory     = "/var/tmp/jobs"
def oauthEnabled      = false
def samlEnabled       = false
def gwavaEnabled      = false
def LDAPEnabled       = false
def transmartURL      = "http://localhost:${System.getProperty('server.port', '8080')}/transmart"


// Personalization

// Project name
com.recomdata.projectName = "Test tranSMART Server"
// name and URL of the supporter entity shown on the welcome page
com.recomdata.providerName = "Bioinformatics Core @ LCSB"
com.recomdata.providerURL = "https://uni.lu/lcsb"
// Application logo
com.recomdata.largeLogo = "transmartlogo.jpg"
// Application search logo
com.recomdata.smallLogo="transmartlogosmall.jpg"
// Contact email
com.recomdata.contactUs = "lcsb-sysadmins@uni.lu"
// Application title
com.recomdata.appTitle = "tranSMART v" + org.transmart.originalConfigBinding.appVersion
// Location of the help pages
com.recomdata.adminHelpURL = "$transmartURL/help/adminHelp/default.htm"
// Bugreport URL
com.recomdata.bugreportURL = "https://jira.transmartfoundation.org"
// Email address of the administrator to contact
com.recomdata.administrator="lcsb-sysadmins@uni.lu"
// Site administrator contact email address
com.recomdata.adminEmail = "lcsb-sysadmins@uni.lu"
// Metadata view
com.recomdata.view.studyview = 'studydetail'
com.recomdata.plugins.resultSize = 5000


// Login and password policy

// Session timeout and heartbeat frequency (ping interval)
// Maximum concurrent sessions for a user (-1: unlimited)
// org.transmartproject.maxConcurrentUserSessions = 10

// Not enabled by default (see Config-extra.php.sample)
//com.recomdata.passwordstrength.pattern
//com.recomdata.passwordstrength.description

// Whether to enable guest auto login.
// If it's enabled no login is required to access tranSMART.
com.recomdata.guestAutoLogin = true
environments { development { com.recomdata.guestAutoLogin = true } }

// Guest account user name - if guestAutoLogin is true, this is the username of
// the account that tranSMART will automatically authenticate users as. This will
// control the level of access anonymous users will have (the access will match
// that of the account specified here).
com.recomdata.guestUserName = 'guest'

bruteForceLoginLock {
    allowedNumberOfAttempts = 5
    lockTimeInMinutes = 10
}

// Password strength criteria, please change description accordingly
//com.recomdata.passwordstrength.pattern = ~/^.*(?=.{8,})(?=.*[a-z])(?=.*[A-Z])(?=.*[\d])(?=.*[\W]).*$/

// Password strength regex that is used to test user's passwords that are entered by themselves.
// Take care to change org.transmartproject.app.user.ChangePasswordCommand.newPassword.lowPasswordStrength
// variable inside messages.properties file of web app.
/*
user.password.strength.regex = '''(?x)
^
(?=.*[A-Z])      #Ensure string has an uppercase letter.
(?=.*[!@\#$&*]) #Ensure string has one special case letter.
(?=.*[0-9])      #Ensure string has a digit.
.{8,}            #Ensure string length is not less then 8.
$'''
*/

//Alternative color scheme for aCGH BED tracks.
//Current colors are captured from cghCall R package.
//Although do not correspond exactly.
/*
dataExport {
    bed {
        acgh {
            rgbColorScheme {
                //white
                invalid       = [255, 255, 255]
                //red
                loss          = [205,   0,   0]
                //dark
                normal        = [ 10,  10,  10]
                //green
                gain          = [  0, 255,   0]
                //dark green
                amplification = [  0, 100,   0]
            }
        }
    }
}
*/

// Password strength description, please change according to pattern
//com.recomdata.passwordstrength.description =
//    'It should contain a minimum of 8 characters including at least ' +
//    '1 upper and 1 lower case letter, 1 digit and 1 special character.'


// HTTP session variables
environments {
    development {
        com.recomdata.sessionTimeout = Integer.MAX_VALUE / 1000 as int /* ~24 days */
        com.recomdata.heartbeatLaps = 900
    }
    production {
        if (com.recomdata.guestAutoLogin) {
            com.recomdata.sessionTimeout = Integer.MAX_VALUE / 1000 as int /* ~24 days */
            com.recomdata.heartbeatLaps = 900
        } else {
            com.recomdata.sessionTimeout = 3600
            com.recomdata.heartbeatLaps = 30
        }
    }
}


// User Interface setup
ui {
    tabs {
        //Search was not part of 1.2. It's not working properly. You need to set `show` to `true` to see it on UI
        search.show = false
        browse.hide = true
        sampleExplorer.hide = false
        geneSignature.hide = true
        gwas.hide = true
        uploadData.hide = true
        datasetExplorer {
            gridView.hide = false
            dataExport.hide = true
            dataExportJobs.hide = true
            // Note: by default the analysisJobs panel is NOT shown
            // Currently, it is only used in special cases
            analysisJobs.show = false
            workspace.hide = false
        }

    }
}


// Variables checks
environments { production {
    if (transmartURL.startsWith('http://localhost:')) {
        println "[WARN] transmartURL not overridden. Some settings (e.g. help page) may be wrong"
    }
} }

// Logs configuration
import org.apache.log4j.DailyRollingFileAppender
import org.transmart.logging.ChildProcessAppender
import org.transmart.logging.JsonLayout

log4j = {
    environments {
        development {
            root {
                info 'stdout'
            }

            // for a less verbose startup & shutdown
            warn  'org.codehaus.groovy.grails.commons.spring'
            warn  'org.codehaus.groovy.grails.orm.hibernate.cfg'
            warn  'org.codehaus.groovy.grails.domain.GrailsDomainClassCleaner'

            debug 'org.transmartproject'
            debug 'com.recomdata'
            debug 'grails.app.controllers'
            debug 'grails.app.services'
            debug 'grails.app.domain'
            debug 'grails.app.services.com.recomdata'
            debug 'grails.app.services.org.transmartproject'
            debug 'grails.app.controllers.com.recomdata'
            debug 'grails.app.controllers.org.transmartproject'
            debug 'grails.app.domain.com.recomdata'
            debug 'grails.app.domain.org.transmartproject'
            // debug 'org.springframework.security'
            // (very verbose) debug  'org.grails.plugin.resource'
        }
        production {
            def logDirectory = "${catalinaBase}/logs".toString()
            appenders {
                rollingFile(name: 'transmart',
                            file: "${logDirectory}/transmart.log",
                            layout: pattern(conversionPattern: '%d{dd-MM-yyyy HH:mm:ss,SSS} %5p %c{1} - %m%n'),
                            maxFileSize: '100MB')
                appender new DailyRollingFileAppender(
                    name: 'fileAuditLogger',
                    datePattern: "'.'yyyy-MM-dd",
                    fileName: "${logDirectory}/audit.log",
                    layout: pattern(conversionPattern: '%d{dd-MM-yyyy HH:mm:ss,SSS} %5p %c{1} - %m%n')
                )
            }
            root {
                warn 'transmart'
            }
            trace additivity: false, fileAuditLogger: 'org.transmart.audit'
            trace transmart: 'org.transmart.audit'
            debug 'org.transmartproject'
            debug 'com.recomdata'
            debug 'grails.app.services.com.recomdata'
            debug 'grails.app.services'
            debug 'grails.app.services.transmartapp'
            debug 'grails.app.services.org.transmartproject'
            debug 'grails.app.controllers.com.recomdata'
            debug 'grails.app.controllers.org.transmartproject'
            debug 'grails.app.domain.com.recomdata'
            debug 'grails.app.domain.org.transmartproject'
         }
    }
}


// Solr configuration
environments {
    development {
        com.rwg.solr.scheme = 'http'
        com.rwg.solr.host   = 'localhost:8983'
        com.rwg.solr.path   = '/solr/rwg/select/'
    }
    production {
        com.rwg.solr.scheme = 'http'
        com.rwg.solr.host   = 'localhost:' + solrPort
        com.rwg.solr.path   = '/solr/rwg/select/'
    }
}

com.rwg.solr.browse.path    = '/solr/browse/select/'
com.rwg.solr.update.path    = '/solr/browse/dataimport/'
com.recomdata.solr.baseURL  = "${com.rwg.solr.scheme}://${com.rwg.solr.host}" +
                             "${new File(com.rwg.solr.browse.path).parent}"

def fileStoreDirectory      = new File(System.getenv('HOME'), '.grails/transmart-filestore')
def fileImportDirectory     = new File(System.getProperty("java.io.tmpdir"), 'transmart-fileimport')
com.recomdata.FmFolderService.filestoreDirectory = fileStoreDirectory.absolutePath
com.recomdata.FmFolderService.importDirectory = fileImportDirectory.absolutePath

[fileStoreDirectory, fileImportDirectory].each {
    if (!it.exists()) {
        it.mkdir()
    }
}


// Search tool configuration

// Lucene index location for documentation search
com.recomdata.searchengine.index = searchIndex
// Sample Explorer configuration
// This is an object to dictate the names and 'pretty names' of the SOLR fields.
// Optionally you can set the width of each of the columns when rendered.
sampleExplorer {
    fieldMapping = [
        columns:[
            [header:'ID', dataIndex:'id', mainTerm: true, showInGrid: true, width:20],
            [header:'trial name', dataIndex:'trial_name', mainTerm: true, showInGrid: true, width:20],
            [header:'barcode', dataIndex:'barcode', mainTerm: true, showInGrid: true, width:20],
            [header:'plate id', dataIndex:'plate_id', mainTerm: true, showInGrid: true, width:20],
            [header:'patient id', dataIndex:'patient_id', mainTerm: true, showInGrid: true, width:20],
            [header:'external id', dataIndex:'external_id', mainTerm: true, showInGrid: true, width:20],
            [header:'aliquot id', dataIndex:'aliquot_id', mainTerm: true, showInGrid: true, width:20],
            [header:'visit', dataIndex:'visit', mainTerm: true, showInGrid: true, width:20],
            [header:'sample type', dataIndex:'sample_type', mainTerm: true, showInGrid: true, width:20],
            [header:'description', dataIndex:'description', mainTerm: true, showInGrid: true, width:20],
            [header:'comment', dataIndex:'comment', mainTerm: true, showInGrid: true, width:20],
            [header:'location', dataIndex:'location', mainTerm: true, showInGrid: true, width:20],
            [header:'organism', dataIndex:'source_organism', mainTerm: true, showInGrid: true, width:20]
        ]
    ]
    resultsGridHeight = 100
    resultsGridWidth = 100
    idfield = 'id'
}

edu.harvard.transmart.sampleBreakdownMap = [
    "aliquot_id":"Aliquots in Cohort"
]


// Solr configuration for the Sample Explorer
com { recomdata { solr {
    maxNewsStories = 10
    maxRows = 10000
}}}


// Dataset Explorer configuration
com { recomdata { datasetExplorer {
    // set to 'true' (quotes included) to enable gene pattern integration
    genePatternEnabled = 'false'
    // The tomcat URL that gene pattern is deployed within -usually it's proxyed through apache
    genePatternURL = 'http://localhost'
    // Gene Pattern real URL with port number
    genePatternRealURLBehindProxy = 'http://localhost'
    // default Gene pattern user to start up - each tranSMART user will need a separate user account to be created in Gene Pattern
    genePatternUser = 'biomart'
    // Absolute path to PLINK executables
    plinkExcutable = '/usr/local/bin/plink'
} } }


// RModules & Data Export Configuration
environments {
    // This is to target a remote Rserve. Bear in mind the need for shared network storage
    RModules.host = "127.0.0.1"
    RModules.port = 6340
    // This is not used in recent versions; the URL is always /analysisFiles/
    RModules.imageURL = "/tempImages/"

    production {
        // The working directory for R scripts, where the jobs get created and
        // output files get generated
        RModules.tempFolderDirectory = jobsDirectory
        RModules.transferImageFile = false
    }

    development {
        RModules.tempFolderDirectory = "/tmp"
        /* we don't need to specify temporaryImageDirectory, because we're not copying */
        RModules.transferImageFile = false
    }

    // Used to access R jobs parent directory outside RModules (e.g. data export)
    com.recomdata.plugins.tempFolderDirectory = RModules.tempFolderDirectory
}

// GWAS Configuration
com.recomdata.dataUpload.appTitle="Upload data to tranSMART"
com.recomdata.dataUpload.stageScript="run_analysis_stage"
// Directory path of com.recomdata.dataUpload.stageScript
def gwasEtlDirectory = new File(System.getenv('HOME'), '.grails/transmart-gwasetl')
// Directory to hold GWAS file uploads
def gwasUploadsDirectory = new File(System.getenv('HOME'), '.grails/transmart-datauploads')
// Directory to preload with template files with names <type>-template.txt
def gwasTemplatesDirectory = new File(System.getenv('HOME'), '.grails/transmart-templates')
com.recomdata.dataUpload.templates.dir = gwasTemplatesDirectory.absolutePath
com.recomdata.dataUpload.uploads.dir = gwasUploadsDirectory.absolutePath
com.recomdata.dataUpload.etl.dir = gwasEtlDirectory.absolutePath

[gwasTemplatesDirectory, gwasUploadsDirectory, gwasEtlDirectory].each {
    if (!it.exists()) {
        it.mkdir()
    }
}

// Misc Configuration

// This can be used to debug JavaScript callbacks in the dataset explorer in
// Chrome. Unfortunately, it also sometimes causes chrome to segfault
com.recomdata.debug.jsCallbacks = 'false'
environments {
    production {
        com.recomdata.debug.jsCallbacks = 'false'
    }
}

grails.resources.adhoc.excludes = [ '/images' + RModules.imageURL + '**' ]

// Adding properties to the Build information panel
buildInfo { properties {
   include = [ 'app.grails.version', 'build.groovy' ]
   exclude = [ 'env.proc.cores' ]
} }


// Spring Security configuration
grails { plugin { springsecurity {
    // customized user GORM class
    userLookup.userDomainClassName = 'org.transmart.searchapp.AuthUser'
    // customized password field
    userLookup.passwordPropertyName = 'passwd'
    // customized user /role join GORM class
    userLookup.authorityJoinClassName = 'org.transmart.searchapp.AuthUser'
    // customized role GORM class
    authority.className = 'org.transmart.searchapp.Role'
    // request map GORM class name - request map is stored in the db
    requestMap.className = 'org.transmart.searchapp.Requestmap'
    // requestmap in db
    securityConfigType = grails.plugin.springsecurity.SecurityConfigType.Requestmap
    // url to redirect after login in
    // just_rest branch provides alternative default via org.transmart.defaultLoginRedirect
    successHandler.defaultTargetUrl = org.transmart.defaultLoginRedirect ?: '/userLanding'
    // logout url
    logout.afterLogoutUrl = '/login/forceAuth'
    // configurable requestmap functionality in transmart is deprecated
    def useRequestMap = false
    if (useRequestMap) {
        // requestmap in db
        securityConfigType = 'Requestmap'
        // request map GORM class name - request map is stored in the db
        requestMap.className = 'org.transmart.searchapp.Requestmap'
    } else {
        securityConfigType = 'InterceptUrlMap'
        def oauthEndpoints = [
              '/oauth/authorize.dispatch': ["isFullyAuthenticated() and (request.getMethod().equals('GET') or request.getMethod().equals('POST'))"],
              '/oauth/token.dispatch':     ["isFullyAuthenticated() and request.getMethod().equals('POST')"],
        ]

        // This looks dangerous and it possibly is (would need to check), but
        // reflects the instructions I got from the developer.
        def gwavaMappings = [
             '/gwasWeb/**'                : ['IS_AUTHENTICATED_ANONYMOUSLY'],
        ]
        interceptUrlMap = [
            '/login/**'                   : ['IS_AUTHENTICATED_ANONYMOUSLY'],
            '/css/**'                     : ['IS_AUTHENTICATED_ANONYMOUSLY'],
            '/js/**'                      : ['IS_AUTHENTICATED_ANONYMOUSLY'],
            '/grails-errorhandler'        : ['IS_AUTHENTICATED_ANONYMOUSLY'],
            '/images/analysisFiles/**'    : ['IS_AUTHENTICATED_REMEMBERED'],
            '/images/**'                  : ['IS_AUTHENTICATED_ANONYMOUSLY'],
            '/static/**'                  : ['IS_AUTHENTICATED_ANONYMOUSLY'],
            '/search/loadAJAX**'          : ['IS_AUTHENTICATED_ANONYMOUSLY'],
            '/analysis/getGenePatternFile': ['IS_AUTHENTICATED_ANONYMOUSLY'],
            '/analysis/getTestFile'       : ['IS_AUTHENTICATED_ANONYMOUSLY'],
            '/requestmap/**'              : ['ROLE_ADMIN'],
            '/role/**'                    : ['ROLE_ADMIN'],
            '/authUser/**'                : ['ROLE_ADMIN'],
            '/secureObject/**'            : ['ROLE_ADMIN'],
            '/accessLog/**'               : ['ROLE_ADMIN'],
            '/authUserSecureAccess/**'    : ['ROLE_ADMIN'],
            '/secureObjectPath/**'        : ['ROLE_ADMIN'],
            '/userGroup/**'               : ['ROLE_ADMIN'],
            '/secureObjectAccess/**'      : ['ROLE_ADMIN'],
            '/oauthAdmin/**'              : ['ROLE_ADMIN'],
            *                             : (oauthEnabled ?  oauthEndpoints : [:]),
            *                             : (gwavaEnabled ?  gwavaMappings : [:]),
            '/**'                         : ['IS_AUTHENTICATED_REMEMBERED'], // must be last
        ]
        rejectIfNoRule = true
    }


    // Password hash algorithm

    //password.algorithm = 'bcrypt'
    // Number of bcrypt rounds
    //password.bcrypt.logrounds = 14

    // Password parameters used with LDAP
    password.algorithm = 'SHA-1'
    password.hash.iterations = 1

    // Spring security – error messages
    errors.login.expired         = 'Your account has expired'
    errors.login.passwordExpired = 'Your password has expired'
    errors.login.disabled        = 'Your login has been disabled'
    errors.login.locked          = 'Your account has been locked'
    errors.login.fail            = 'Login has failed; check the provided credentials'

    // Authentication providers (LDAP and Guest mainly)
    providerNames = ['daoAuthenticationProvider',
        'anonymousAuthenticationProvider',
        'rememberMeAuthenticationProvider',
    ]

    // OAuth check
    if (oauthEnabled) {
        providerNames << 'clientCredentialsAuthenticationProvider'

        def securedResourcesFilters = [
                'JOINED_FILTERS',
                '-securityContextPersistenceFilter',
                '-logoutFilter',
                '-rememberMeAuthenticationFilter',
                '-basicAuthenticationFilter',
                '-exceptionTranslationFilter',
        ].join(',')

        filterChain.chainMap = [
                '/oauth/token': [
                        'JOINED_FILTERS',
                        '-oauth2ProviderFilter',
                        '-securityContextPersistenceFilter',
                        '-logoutFilter',
                        '-rememberMeAuthenticationFilter',
                        '-exceptionTranslationFilter',
                ].join(','),
                '/studies/**': securedResourcesFilters,
                '/observations/**': securedResourcesFilters,
                '/patient_sets/**': securedResourcesFilters,
                '/oauth/inspectToken': securedResourcesFilters,
                '/**': [
                        'JOINED_FILTERS',
                        '-statelessSecurityContextPersistenceFilter',
                        '-oauth2ProviderFilter',
                        '-clientCredentialsTokenEndpointFilter',
                        '-basicAuthenticationFilter',
                        '-oauth2ExceptionTranslationFilter'
                ].join(','),
        ]

        grails.exceptionresolver.params.exclude = ['password', 'client_secret']

        def glowingBearRedirectUris = [
                transmartURL - ~/transmart\/?$/ + 'connections',
        ]
        // for dev, node reverse proxy runs on 8001
        glowingBearRedirectUris << 'http://localhost:8001/connections'

        oauthProvider {
            authorization.requireRegisteredRedirectUri = true
            authorization.requireScope = false

            clients = [
                    [
                        clientId: 'api-client',
                        clientSecret: 'api-client',
                        authorities: ['ROLE_CLIENT'],
                        scopes: ['read', 'write'],
                        authorizedGrantTypes: ['authorization_code', 'refresh_token'],
                        redirectUris: [(transmartURL - ~'\\/$') + '/oauth/verify'],
                    ],
                    [
                        clientId: 'glowingbear-js',
                        clientSecret: '',
                        authorities: ['ROLE_CLIENT'],
                        scopes: ['read', 'write'],
                        authorizedGrantTypes: ['implicit', 'password'],
                        redirectUris: glowingBearRedirectUris,
                    ],
            ]
        } }

    // LDAP check
    if (LDAPEnabled) { providerNames << 'ldapAuthProvider' }

} } }


// LDAP configuration
if (LDAPEnabled) {
    org.transmart.security.spnegoEnabled = true
    grails { plugin { springsecurity { ldap {
        active = true

        context {
            // Address of the LDAP server
            server = 'ldap://10.240.6.51'
            // Distinguished Name (DN) to authenticate with
            managerDn = 'uid=admin,cn=users,cn=accounts,dc=novalocal,dc=novalocal'
            // Password to authenticate with
            managerPassword = 'secret'
            // Whether or not integrate internal roles. Blurry notion, documentation missing
            allowInternaRoles = 'false'
        }

        search {
            // Context name to search in, relative to the base of the configured ContextSource, e.g. 'dc=example,dc=com', 'ou=users,dc=example,dc=com'
            base = 'cn=users,cn=accounts,dc=novalocal,dc=novalocal'
            // The filter expression used in the user search
            filter = '(uid={0})'
        }

        // Names of attribute ids to return; use null to return all and an empty list to return none
        authenticator.attributesToReturn = ['uid', 'mail', 'cn']

        authorities {
            // The base DN from which the search for group membership should be performed
            groupSearchBase = 'ou=transmart_vm1,ou=project_1,ou=transmart,dc=novalocal,dc=novalocal'
            // The pattern to be used for the user search. {0} is the user's DN
            groupSearchFilter = 'memberUid={1}'
            // Whether PartialResultExceptions should be ignored in searches, typically used with Active Directory since AD servers often have a problem with referrals
            ignorePartialResultException = true
            // Whether to infer roles based on group membership
            retrieveGroupRoles = true
            // Whether to retrieve additional roles from the database using the User/Role many-to-many
            retrieveDatabaseRoles = false
        }
} } } } }


// SAML Configuration
if (samlEnabled) {
    // don't do assignment to grails.plugin.springsecurity.providerNames
    // see GRAILS-11730
    grails { plugin { springsecurity {
        providerNames << 'samlAuthenticationProvider'
    } } }
    // again, because of GRAILS-11730
    def ourPluginConfig
    grails {
        ourPluginConfig = plugin
    }

    org { transmart { security {
        setProperty('samlEnabled', true) // Clashed with local variable
        ssoEnabled  = "true"

        // URL to redirect to after successful authentication
        successRedirectHandler.defaultTargetUrl = ourPluginConfig.springsecurity.successHandler.defaultTargetUrl
        // URL to redirect to after successful logout
        successLogoutHandler.defaultTargetUrl = ourPluginConfig.springsecurity.logout.afterLogoutUrl

        saml {
            // Service provider details (we)
            sp {
                // ID of the Service Provider
                id = "gustavo-transmart"

                // URL of the service provider. This should be autodected, but it isn't
                url = "http://localhost:8080/transmart"

                // Alias of the Service Provider
                alias = "transmart"

                // Alias of the Service Provider's signing key, see keystore details
                signingKeyAlias = "saml-signing"
                // Alias of the Service Provider's encryption key
                encryptionKeyAlias = "saml-encryption"
            }

            // Metadata file of the provider. We insist on keeping instead of just
            // retrieving it from the provider on startup to prevent transmart from
            // being unable to start due to provider being down. A copy will still be
            // periodically fetched from the provider
            idp.metadataFile = '/home/glopes/idp-local-metadata.xml'

            // Keystore details
            keystore {
                // Generate with:
                //  keytool -genkey -keyalg RSA -alias saml-{signing,encryption} \
                //    -keystore transmart.jks -storepass changeit \
                //    -validity 3602 -keysize 2048
                // Location of the keystore. You can use other schemes, like classpath:resource/samlKeystore.jks
                file = 'file:///home/glopes/transmart.jks'

                // keystore's storepass
                password="changeit"

                // keystore's default key
                defaultKey="saml-signing"

                // Alias of the encryption key in the keystore
                encryptionKey.alias="saml-encryption"
                // Password of the key with above alias in the keystore
                encryptionKey.password="changeit"

                // Alias of the signing key in the keystore
                signingKey.alias="saml-signing"
                // Password of the key with above alias in the keystore
                signingKey.password="changeit"
            }

            // Creation of new users
            createInexistentUsers = "true"
            attribute.username    = "urn:custodix:ciam:1.0:principal:username"
            attribute.firstName   = "urn:oid:2.5.4.42"
            attribute.lastName    = "urn:oid:2.5.4.4"
            attribute.email       = ""
            attribute.federatedId = "personPrincipalName"

            // Suffix of the login filter, saml authentication is initiated when user browses to this url
            entryPoint.filterProcesses = "/saml/login"
            // SAML Binding to be used for above entry point url.
            entryPoint.binding = "urn:oasis:names:tc:SAML:2.0:bindings:HTTP-POST"
            // This property must be set otherwise the default binding is used which, in this configuration, is HTTP-ARTIFACT
            entryPoint.defaultAssertionConsumerIndex = "1"

            // Suffix of the Service Provider's metadata, this url needs to be configured on IDP
            metadata.filterSuffix = "/saml/metadata"
            // Id of the spring security's authentication manager
            authenticationManager = "authenticationManager"
            // Whether sessions should be invalidated after logout
            logout.invalidateHttpSession = "true"
            // Id of the spring security user service that should be called to fetch users.
            saml.userService = "org.transmart.FederatedUserDetailsService"
        }
} } } }
else { // if (!samlEnabled)
    org { transmart { security {
        setProperty('samlEnabled', false) // Clashed with local variable
} } } }


// GWAVA configuration
if (gwavaEnabled) {
    // assume deployment alongside transmart
    com { recomdata { rwg { webstart {
        def url       = new URL(transmartURL)
        codebase      = "$url.protocol://$url.host${url.port != -1 ? ":$url.port" : ''}/gwava"
        jar           = './ManhattanViz2.1g.jar'
        mainClass     = 'com.pfizer.mrbt.genomics.Driver'
        gwavaInstance = 'transmartstg'
        transmart.url = transmartURL - ~'\\/$'
    } } } }
    com { recomdata { rwg { qqplots {
        cacheImages = new File(jobsDirectory, 'cachedQQplotImages').toString()
    } } } }
}


// Quartz jobs configuration

// start delay for the sweep job
com.recomdata.export.jobs.sweep.startDelay = 60000 // d*h*m*s*1000
// repeat interval for the sweep job
com.recomdata.export.jobs.sweep.repeatInterval = 86400000 // d*h*m*s*1000
// specify the age of files to be deleted (in days)
com.recomdata.export.jobs.sweep.fileAge = 3


// EOF You MUST leave this at the end
org.transmart.configFine = true

// vim: set fdm=marker et ts=4 sw=4 filetype=groovy ai: