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A server that exposes Pathling functionality through a FHIR API.
There is a newer version: 7.0.1
spring:
  profiles:
    active:
      - core
      - server
  banner:
    location: classpath:banner.txt

# Actuator endpoints let you monitor and interact with your application.
# 
management:
  server:
    port: 8081
  endpoints:
    web:
      exposure:
        include: "health,prometheus"
  endpoint:
    health:
      probes:
        add-additional-paths: true

pathling:
  # Controls the description of this server as displayed within the FHIR CapabilityStatement.
  implementationDescription: Yet Another Pathling Server

  # If this variable is set, all errors will be reported to a Sentry service, e.g.
  # `https://[email protected]/123456`.
  # sentryDsn: [Sentry DSN]

  # This variable sets the environment that each Sentry report is tagged with.
  # sentryEnvironment: [environment]

  spark:
    # The name that Pathling will be identified as within the Spark cluster.
    appName: pathling

  storage:
    # The base URL at which Pathling will look for data files, and where it will save data received
    # within import requests. Can be an Amazon S3 (s3://), HDFS (hdfs://) or filesystem (file://)
    # URL.
    warehouseUrl: file:///usr/share/warehouse

    # The subdirectory within the warehouse path used to read and write data.
    databaseName: default

    # This controls whether the built-in caching within Spark is used for resource datasets
    # It may be useful to turn this off for large datasets in memory-constrained environments.
    cacheDatasets: true

    # When a table is updated, the number of partitions is checked. If the number exceeds this
    # threshold, the table will be repartitioned back to the default number of partitions. This
    # prevents large numbers of small updates causing poor subsequent query performance.
    compactionThreshold: 10

  query:
    # Setting this option to true will enable additional logging relating to the query plan used to
    # execute queries.
    explainQueries: false

    # This controls whether the built-in caching within Spark is used for search results.
    # It may be useful to turn this off for large datasets in memory-constrained environments.
    cacheResults: true

  auth:
    # Enables authorization.
    enabled: false

    # Configures the issuing domain for bearer tokens, which will be checked against the claims
    # within incoming bearer tokens.
    # issuer: [issuer]

    # Configures the audience for bearer tokens, which is the FHIR endpoint that tokens are
    # intended to be authorised for.
    # audience: [audience]

    # Provides the URL which will be advertised as the authorization endpoint.
    # authorizeUrl: [authorization URL]

    # Provides the URL which will be advertised as the token endpoint.
    # tokenUrl: [token URL]

    # Provides the URL which will be advertised as the token revocation endpoint.
    # revokeUrl: [token revocation URL]

    ga4ghPassports:
      # When GA4GH passport authentication is enabled, this option configures the identifier system
      # that is used to identify and control access to patient data.
      patientIdSystem: http://www.australiangenomics.org.au/id/study-number

      # When GA4GH passport authentication is enabled, this option configures the list of endpoints
      # that are allowed to issue visas.
      allowedVisaIssuers: [ ]

  # This section configures HTTP caching response headers.
  httpCaching:
    # A list of values to return within the Vary header.
    vary:
      - Accept
      - Accept-Encoding
      - Prefer
      - Authorization
    # A list of values to return within the Cache-Control header, for cacheable responses.
    cacheableControl:
      - must-revalidate
      - max-age=1
    # A list of values to return within the Cache-Control header, for uncacheable responses.
    uncacheableControl:
      - no-store

  # This section configures the CORS functionality of the server.
  # For more information, see: https://developer.mozilla.org/en-US/docs/Web/HTTP/CORS
  cors:
    allowedOrigins: [ ]
    allowedOriginPatterns: [ ]
    allowedMethods:
      - OPTIONS
      - GET
      - POST
    allowedHeaders:
      - Content-Type
      - Authorization
      - Prefer
    exposedHeaders:
      - Content-Location
      - X-Progress
    maxAge: 600

  import:
    allowableSources:
      - "file:///usr/share/staging"

  # This section configures the server's support asynchronous processing of HTTP requests.
  async:
    # Enables asynchronous processing for those operations that support it,
    # when explicitly requested by a HTTP client.
    enabled: true
    
    #  A subset of `pathling.httpCaching.vary` HTTP headers, which should 
    #  be  excluded from determining that asynchronous requests are the equivalent
    #  and can be routed to the same asynchronous job.
    varyHeadersExcludedFromCacheKey:
      - Accept
      - Accept-Encoding

# Use this section to set or override any Spark configuration parameter. Tuning these parameters is
# essential to get the optimal performance for your dataset.
# Here is the full list: https://spark.apache.org/docs/latest/configuration.html
spark:
  master: local[*]
  sql:
    adaptive:
      enabled: true
      coalescePartitions:
        enabled: true
    extensions: io.delta.sql.DeltaSparkSessionExtension
    catalog:
      spark_catalog: org.apache.spark.sql.delta.catalog.DeltaCatalog
  databricks:
    delta:
      schema:
        autoMerge:
          enabled: true
  scheduler:
    mode: FAIR

# Use this section to set or override configuration relating to S3 configuration.
# See: https://hadoop.apache.org/docs/stable/hadoop-aws/tools/hadoop-aws/index.html
fs:
  s3a:
    aws:
    # credentials:
    #   provider: org.apache.hadoop.fs.s3a.AnonymousAWSCredentialsProvider
    #   provider: org.apache.hadoop.fs.s3a.auth.AssumedRoleCredentialProvider
    #
    # For use with: SimpleAWSCredentialsProvider
    # access:
    #   key: [access key]
    # secret:
    #   key: [secret key]
    #
    # For use with: AssumedRoleCredentialProvider
    # assumed:
    #   role:
    #     arn: [role ARN]
    #
    connection:
      maximum: 100
    committer:
      name: magic
      magic:
        enabled: true