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ArachneNodeAPI

Arachne Data Node is a component that facilitates connection and communication between local databases and Arachne Central

Installation

Prerequisites

For building and run the Data Node please install following applications:

Running with Authenticator in a standalone mode

  • Create database to store users (or use another authentication provided by Authenticator)
  • Create users table and populate it (or use database from the ArachneCentralAPI)
  • Apply create if not exists user registration strategy by (see about strategies below)
-Dauthenticator.user.registrationStrategy=CREATE_IF_NOT_EXISTS
  • Run application applying the following parameters:
-Dauthenticator.methods.db.service=org.ohdsi.authenticator.service.jdbc.JdbcAuthService
-Dauthenticator.methods.db.config.jdbcUrl=jdbc:postgresql://localhost:5432/arachne_portal
-Dauthenticator.methods.db.config.username=user
-Dauthenticator.methods.db.config.password=secret
-Dauthenticator.methods.db.config.query="select password, id, firstname, lastname, email from users_data where email=:username"
-Dauthenticator.methods.db.config.passwordEncoder=org.springframework.security.crypto.bcrypt.BCryptPasswordEncoder
-Dauthenticator.methods.db.config.fieldsToExtract.firstName=firstname
-Dauthenticator.methods.db.config.fieldsToExtract.lastName=lastname
-Dauthenticator.methods.db.config.fieldsToExtract.id=T(com.odysseusinc.arachne.commons.utils.UserIdUtils).idToUuid(T(java.lang.Long).valueOf(id))
-Dauthenticator.methods.db.config.fieldsToExtract.email=email
-Dsecurity.method=db

Stand-alone mode

The configuration parameter datanode.runMode is used to set Data Node running mode. There are two value supported:

  • NETWORK which is default, sets running in network mode and requires communication with Central
  • STANDALONE sets running in standalone mode when communication with Central is not supported and some functions become unavailable

Features disabled in Stand-alone mode

  • All operations related to Atlas
  • Data Source publishing
  • Removal of Data Sources of Data Sources which have been published before
  • Import and Re-import of Achilles results
  • Adding new users from Central

Note: it's prohibited to switch from Standalone to Network mode when there are some offline entities, such as users, has been created in standalone mode.

User registration strategies

There are two user registration strategies:

  • CREATE_IF_FIRST - means first user succcesfully logged in registered by system and became Data Node administrator. Other users should be added by administrator manually using Admin section.
  • CREATE_IF_NOT_EXISTS - means any user who logged in would be registered if one's not registered before. This useful when using external authentication source like Active Directory. When external authentication source is used then Admin page could not be used to add users since don't know where to find users.