Page tree

Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

The file configuration.yml contains the main configuration of OpenCGA Catalog.


Code Block
titleconfiguration.yml
linenumberstrue
collapsetrue
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.

Code Block
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:

Table of Contents
indent20px