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The file configuration.yml contains the main configuration of OpenCGA Catalog.
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logLevel: "INFO" logFile: null openRegister: false userDefaultQuota: 200000 databasePrefix: ${OPENCGA.DB.PREFIX} dataDir: ${OPENCGA.USER.WORKSPACE} tempJobsDir: ${OPENCGA.JOBS.DIR} toolDir: ${OPENCGA.TOOLS.DIR} admin: password: "" email: "" audit: maxDocuments: 20000000 # Maximum number of documents that will be created in the audit collection. maxSize: 100000000000 # Maximum size that the audit collection will have in bytes. javaClass: "" # Java class of the audit implementation to be used to audit. exclude: [] # Array of resource:action to select pairwise resource-actions to be excluded for audit purposes. monitor: daysToRemove: 30 executionDaemonInterval: 4000 # number of milliseconds between checks fileDaemonInterval: 8000 # number of milliseconds between checks port: ${OPENCGA.MONITOR.PORT} execution: mode: ${OPENCGA.EXECUTION.MODE} defaultQueue: "" availableQueues: "" toolsPerQueue: {} email: host: ${OPENCGA.MAIL.HOST} port: ${OPENCGA.MAIL.PORT} user: ${OPENCGA.MAIL.USER} password: ${OPENCGA.MAIL.PASSWORD} from: "" ssl: false catalog: # offset: Starting point for the catalog internal ids. Use a big offset number (1000000 for instance) if you plan to use numerical ids # for names or aliases of any entity. offset: 0 database: hosts: - ${OPENCGA.CATALOG.DB.HOSTS} user: ${OPENCGA.CATALOG.DB.USER} password: ${OPENCGA.CATALOG.DB.PASSWORD} options: authenticationDatabase: ${OPENCGA.CATALOG.DB.AUTHENTICATION_DATABASE} connectionsPerHost: ${OPENCGA.CATALOG.DB.CONNECTIONS_PER_HOST} authentication: # Session expiration time in seconds expiration: 3600 # LDAP configuration example #authenticationOrigins: #- id: ldap # Any id # type: LDAP # At the moment, we only support LDAP # host: ldap://localhost:9000 # options: # usersSearch: dc=ge,dc=co,dc=uk # Base search to look for the users # groupsSearch: ou=general,ou=groups,dc=ge,dc=co,dc=uk # Base search to look for the groups server: rest: port: ${OPENCGA.SERVER.REST.PORT} logFile: null defaultLimit: 2000 maxLimit: 5000 grpc: port: ${OPENCGA.SERVER.GRPC.PORT} logFile: null |
The file is divided into several sections that will be explained in detail.
Root file
The first sections of the file logLevel and logFile should contain the level of the logs that will be reported (info, debug, warning, error) and whether this logs should be streamed to a file or via the standard output.
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logLevel: "INFO" #
logFile: null
openRegister: false
userDefaultQuota: 200000
databasePrefix: ${OPENCGA.DB.PREFIX}
dataDir: ${OPENCGA.USER.WORKSPACE}
tempJobsDir: ${OPENCGA.JOBS.DIR}
toolDir: ${OPENCGA.TOOLS.DIR} |
Table of Contents:
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