apollo-config.groovy

environments {
    development {
    }
    test {
    }
    production {
        dataSource {
            dbCreate = "update"
            username = System.getenv("WEBAPOLLO_DB_USERNAME")
            password = System.getenv("WEBAPOLLO_DB_PASSWORD")

            driverClassName = "org.postgresql.Driver"
            dialect = "org.hibernate.dialect.PostgresPlusDialect"
            url = System.getenv("WEBAPOLLO_DB_URI")

            properties {
                // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation
                jmxEnabled                    = false
                initialSize                   = 5
                maxActive                     = 50
                minIdle                       = 5
                maxIdle                       = 25
                maxWait                       = 10000
                maxAge                        = 10 * 60000
                timeBetweenEvictionRunsMillis = 5000
                minEvictableIdleTimeMillis    = 60000
                validationQuery               = "SELECT 1"
                validationQueryTimeout        = 3
                validationInterval            = 15000
                testOnBorrow                  = true
                testWhileIdle                 = true
                testOnReturn                  = false
                jdbcInterceptors              = "ConnectionState"
                defaultTransactionIsolation   = java.sql.Connection.TRANSACTION_READ_COMMITTED
            }
        }
        dataSource_chado {
            dbCreate = "update"
            username = System.getenv("WEBAPOLLO_CHADO_DB_USERNAME")
            password = System.getenv("WEBAPOLLO_CHADO_DB_PASSWORD")

            driverClassName = "org.postgresql.Driver"
            dialect = "org.hibernate.dialect.PostgresPlusDialect"
            url = System.getenv("WEBAPOLLO_CHADO_DB_URI")

            properties {
                // See http://grails.org/doc/latest/guide/conf.html#dataSource for documentation
                jmxEnabled                    = false
                initialSize                   = 5
                maxActive                     = 50
                minIdle                       = 5
                maxIdle                       = 25
                maxWait                       = 10000
                maxAge                        = 10 * 60000
                timeBetweenEvictionRunsMillis = 5000
                minEvictableIdleTimeMillis    = 60000
                validationQuery               = "SELECT 1"
                validationQueryTimeout        = 3
                validationInterval            = 15000
                testOnBorrow                  = true
                testWhileIdle                 = true
                testOnReturn                  = false
                jdbcInterceptors              = "ConnectionState"
                defaultTransactionIsolation   = java.sql.Connection.TRANSACTION_READ_COMMITTED
            }
        }
    }
}

apollo {
    default_minimum_intron_size = System.getenv("WEBAPOLLO_MINIMUM_INTRON_SIZE") ? System.getenv("WEBAPOLLO_MINIMUM_INTRON_SIZE").toInteger() : 1
    history_size = System.getenv("WEBAPOLLO_HISTORY_SIZE") ? System.getenv("WEBAPOLLO_HISTORY_SIZE").toInteger() : 0
    overlapper_class = System.getenv("WEBAPOLLO_OVERLAPPER_CLASS") ?: "org.bbop.apollo.sequence.OrfOverlapper"
    use_cds_for_new_transcripts = System.getenv("WEBAPOLLO_CDS_FOR_NEW_TRANSCRIPTS").equals("true")
    feature_has_dbxrefs = System.getenv("WEBAPOLLO_FEATURE_HAS_DBXREFS").equals("true")
    feature_has_attributes = System.getenv("WEBAPOLLO_FEATURE_HAS_ATTRS").equals("true")
    feature_has_pubmed_ids = System.getenv("WEBAPOLLO_FEATURE_HAS_PUBMED").equals("true")
    feature_has_go_ids = System.getenv("WEBAPOLLO_FEATURE_HAS_GO").equals("true")
    feature_has_comments = System.getenv("WEBAPOLLO_FEATURE_HAS_COMMENTS").equals("true")
    feature_has_status = System.getenv("WEBAPOLLO_FEATURE_HAS_STATUS").equals("true")
    translation_table = "/config/translation_tables/ncbi_" + (System.getenv("WEBAPOLLO_TRANSLATION_TABLE") ?: "1") + "_translation_table.txt"
    get_translation_code = System.getenv("WEBAPOLLO_TRANSLATION_TABLE") ? System.getenv("WEBAPOLLO_TRANSLATION_TABLE").toInteger() : 1
    user_pure_memory_store = true
    is_partial_translation_allowed = false // unused so far
    export_subfeature_attrs = System.getenv("WEBAPOLLO_EXPORT_SUBFEATURE_ATTRS").equals("true")

    // settings for Chado export
    // set chado_export_fasta_for_sequence if you want the reference sequence FASTA to be exported into the database
    // Note: Enabling this feature can be memory intensive
    chado_export_fasta_for_sequence = System.getenv("WEBAPOLLO_CHADO_EXPORT_FASTA_SEQUENCE").equals("true")
    // set chado_export_fasta_for_cds if you want the CDS FASTA to be exported into the database
    chado_export_fasta_for_cds = System.getenv("WEBAPOLLO_CHADO_EXPORT_FASTA_CDSS").equals("true")

    // TODO: should come from config or via preferences database
    splice_donor_sites = System.getenv("WEBAPOLLO_SPLICE_DONOR_SITES") ? System.getenv("WEBAPOLLO_SPLICE_DONOR_SITES").split(",") : ["GT"]
    splice_acceptor_sites = System.getenv("WEBAPOLLO_SPLICE_ACCEPTOR_SITES") ? System.getenv("WEBAPOLLO_SPLICE_ACCEPTOR_SITES").split(",") : ["AG"]
    gff3.source = System.getenv("WEBAPOLLO_GFF3_SOURCE") ?: "."

    google_analytics = System.getenv("WEBAPOLLO_GOOGLE_ANALYTICS_ID")

    admin{
        username = System.getenv("APOLLO_ADMIN_EMAIL") ?: "admin@local.host"
        password = System.getenv("APOLLO_ADMIN_PASSWORD") ?: "password"
        firstName = System.getenv("APOLLO_ADMIN_FIRST_NAME") ?: "Ad"
        lastName = System.getenv("APOLLO_ADMIN_LAST_NAME") ?: "min"
    }

    authentications = [
        [
            "name":"Remote User Authenticator",
            "className":"remoteUserAuthenticatorService",
            "active":true
        ],
        [
            "name":"Username Password Authenticator",
            "className":"usernamePasswordAuthenticatorService",
            "active":true
        ]
    ]

}

jbrowse {
    git {
        url = "https://github.com/GMOD/jbrowse"
        tag = "9d765aecaee02a41844fed11a241fdb4c35fc9f8"
        alwaysPull = true
        alwaysRecheck = true
    }
    plugins {
        NeatHTMLFeatures{
            included = true
        }
        NeatCanvasFeatures{
            included = true
        }
        RegexSequenceSearch{
            included = true
        }
        HideTrackLabels{
            included = true
        }
        GCContent {
            git = 'https://github.com/elsiklab/gccontent'
            branch = 'master'
            alwaysRecheck = "true"
            alwaysPull = "true"
        }
        MyVariantInfo {
            git = 'https://github.com/GMOD/myvariantviewer'
            branch = 'master'
            alwaysRecheck = "true"
            alwaysPull = "true"
        }
        SashimiPlot {
            git = 'https://github.com/cmdcolin/sashimiplot'
            branch = 'master'
            alwaysPull = "true"
        }
    }
}