Chapter 8 - SHRINE's Configuration File

cp shrine-setup/qep-and-adapter-shrine.conf /opt/shrine/tomcat/lib/shrine.conf

shrineHubBaseUrl = "https://shrine-hub.faraway.com:6443" //The shrine hub's URL as observed from this tomcat server
i2b2BaseUrl = "http://i2b2.example.com:9090" 	//The local i2b2's URL as observed from this tomcat server
i2b2Domain = "exampleDomain"
i2b2ShrineProjectName = "SHRINE"

shrine {

  nodeKey = "testNode" //node key to get information from the hub about this node. Your hub administrator will tell you this value
  shrineDatabaseType = "mysql" //can be mysql, sqlserver, oracle

  messagequeue {
    blockingq {
      serverUrl = ${shrineHubBaseUrl}/shrine-api/mom
    }
  }

  webclient {
   domain = ${i2b2Domain}
   name  = ${i2b2ShrineProjectName}
   siteAdminEmail = "email@example.com"
   usernameLabel = "User Name"
   passwordLabel = "User Password"
   defaultNumberOfOntologyChildren = 10000  // the number of children to show when an ontology folder is expanded.
   queryFlaggingInstructions = "Enter instructions for flagging queries here"
   flaggingPlaceholderText = "Enter placeholder text for the query flagging text input field"
   flaggingIconInstructions = "Enter text for when user mouses over the flagging information icon in the header of the Query History here"
  }

  pmEndpoint {
    url = ${i2b2BaseUrl}/i2b2/services/PMService/getServices
  }

  ontEndpoint {
    url = ${i2b2BaseUrl}/i2b2/services/OntologyService
  }
  
  hiveCredentials {
    domain = ${i2b2Domain}
    username = "demo"
    password = "demouser"
    crcProjectId = "Demo"
    ontProjectId = ${i2b2ShrineProjectName}
  }

  breakdownResultOutputTypes {
    PATIENT_AGE_COUNT_XML {
      description = "Age patient breakdown"
    }
    PATIENT_RACE_COUNT_XML {
      description = "Race patient breakdown"
    }
    PATIENT_VITALSTATUS_COUNT_XML {
      description = "Vital Status patient breakdown"
    }
    PATIENT_GENDER_COUNT_XML {
      description = "Gender patient breakdown"
    }
  } //end breakdown section

  hub {
    client {
      serverUrl = ${shrineHubBaseUrl}
    }
  }

  queryEntryPoint {
    broadcasterServiceEndpoint {
      url = ${shrineHubBaseUrl}/shrine/rest/broadcaster/broadcast
    }
  }

  adapter {
    crcEndpoint {
      url = ${i2b2BaseUrl}/i2b2/services/QueryToolService/
    }

    adapterMappingsFileName = "AdapterMappings.csv"
    crcRunQueryTimeLimit = "30 seconds" // in seconds, use quotes. default 30 seconds
  } //end adapter section

  keystore {
    file = "/opt/shrine/shrine.keystore"
    password = "changeit"
    privateKeyAlias = "shrine-node"
    keyStoreType = "JKS"
    caCertAliases = ["shrine-ca"]
  } //end keystore section

  steward {
    createTopicsMode = Approved //the default is Pending - the most secure - but most sites use Approved

    emailDataSteward {
      sendAuditEmails = false  //false to turn off the whole works of emailing the data steward      
	  //interval = "1 day" //Audit researchers daily
      //timeAfterMidnight = "6 hours" //Audit researchers at 6 am. If the interval is less than 1 day, then this delay is ignored.
      //maxQueryCountBetweenAudits = 30 //If a researcher runs more than this many queries since the last audit audit her
      //minTimeBetweenAudits = "30 days" //If a researcher runs at least one query, audit those queries if this much time has passed
  
      //You must provide the email address of the shrine node system admin, to handle bounces and invalid addresses
      //from = "shrine-admin@example.com"
      //You must provide the email address of the data steward
      //to = "shrine-steward@example.com"
  
      //subject = "Audit SHRINE researchers"
      //The baseUrl for the data steward to be substituted in to email text. Must be supplied if it is used in the email text.
      //stewardBaseUrl = "https://example.com:6443/shrine-api/shrine-steward/"
      externalStewardBaseUrl = "https://example.com:6443/shrine-api/shrine-steward/"
  
      //Text to use for the email audit.
      //AUDIT_LINES will be replaced by a researcherLine for each researcher to audit.
      //STEWARD_BASE_URL will be replaced by the value in stewardBaseUrl if available.
      //emailBody = """Please audit the following users at STEWARD_BASE_URL at your earliest convenience: AUDIT_LINES"""
      //note that this can be a multiline message
  
      //Text to use per researcher to audit.
      //FULLNAME, USERNAME, COUNT and LAST_AUDIT_DATE will be replaced with appropriate text.
      //researcherLine = "FULLNAME (USERNAME) has run COUNT queries since LAST_AUDIT_DATE."
    }
  } //end steward section
  
} //end shrine