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DRAFT

Table of Contents

Overview

This document describes the OpenCDS Configuration for version 12.3.x and above.

What's new?

    • Dedicated schemas for describing configuration metadata.
      • Migration tool to migrate configuration schema from the previous version (1.2.x, 1.1.x, etc.) to the new version.
    • REST interface for adding/updating and retrieving the configuration metadata
      • including reloadability of File-based configuration.
    • Backwards compatibility with ClassPath- and File-based configuration.
      • NOT compatible with previous schemas; migration is required.
    • New backend configuration scheme using BerkeleyDB (BDB-JE).
      • This is the only method that is supported via REST.

Schemas

OpenCDS Configuration schemas consist of a base schema and a REST schema.  The REST schema contains the elements that are used for physical configuration metadata (e.g., XML files).

Base Schema

<insert base schema ref here>

REST Schema

<insert rest schema ref here>

Schema Discussion

The REST schema is the entry point for OpenCDS configuration, whether they exist as files on the filesystem or as objects in BerkeleyDB.  The main elements are as follows:

ConceptDeterminationMethods

ConceptDeterminationMethods consists of one or more ConceptDeterminationMethod elements.

Code Block
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titleConceptDeterminationMethods Example
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<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<ns3:conceptDeterminationMethods xmlns:ns2="org.opencds.dss.config.v1_0" xmlns:ns3="org.opencds.dss.config_rest.v1_0">
    <conceptDeterminationMethod code="C45" displayName="NQF" codeSystem="2.16.840.1.113883.3.795.12.1.1" version="1.0">
    ...
    </conceptDeterminationMethod>
    <conceptDeterminationMethod code="C267" displayName="AHRQ" codeSystem="2.16.840.1.113883.3.795.12.1.1" version="1.0">
    ...
    </conceptDeterminationMethod>
    <conceptDeterminationMethod code="C36" displayName="OpenCDS" codeSystem="2.16.840.1.113883.3.795.12.1.1" version="1.0">
    ...
    </conceptDeterminationMethod>
</ns3:conceptDeterminationMethods>

 

ConceptDeterminationMethod

ConceptDeterminationMethod contains concept mappings from local or standard concepts to OpenCDS concepts.  The concept mapping metadata is organized such that toConcept is the OpenCDS concept, while the associated fromConcepts compose the local and standard concepts that are contained in the vMR data.  For each of the local concepts found, OpenCDS will add the OpenCDS concept (the toConcept) to the internal fact lists.

An example ConceptDeterminationMethod is shown below:

Code Block
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titleConceptDeterminationMethod Example
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<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<ns3:conceptDeterminationMethod xmlns:ns2="org.opencds.dss.config.v1_0" xmlns:ns3="org.opencds.dss.config_rest.v1_0" code="C74" displayName="CDC-RD concept determination method" codeSystem="2.16.840.1.113883.3.795.12.1.1" version="1.0">
    <conceptMapping>
        <toConcept code="C88" codeSystem="2.16.840.1.113883.3.795.12.1.1" codeSystemName="OpenCDS concepts" displayName="Result Negative" />
        <fromConcepts codeSystem="2.16.840.1.113883.3.795.12.1.2" codeSystemName="OpenCDS proprietary local" displayName="Result Negative">
            <concept code="NEGATIVE" displayName="Result Negative" />
            <concept code="Negative" displayName="Result Negative" />
            <concept code="negative" displayName="Result Negative" />
            <concept code="NEG" displayName="Result Negative" />
            <concept code="Neg" displayName="Result Negative" />
            <concept code="neg" displayName="Result Negative" />
            <concept code="N" displayName="Result Negative" />
            <concept code="n" displayName="Result Negative" />
            <concept code="Invalid" displayName="Result Negative" />
            <concept code="Indeterminate" displayName="Result Negative" />
            <concept code="Inadequate" displayName="Result Negative" />
            <concept code="Not Detected" displayName="Result Negative" />
        </fromConcepts>
    </conceptMapping>
    <conceptMapping>
        <toConcept code="C273" codeSystem="2.16.840.1.113883.3.795.12.1.1" codeSystemName="OpenCDS concepts" displayName="Strep Pneumo Test For Organism" />
        <fromConcepts codeSystem="2.16.840.1.113883.3.795.12.1.2" codeSystemName="OpenCDS proprietary local" displayName="Streptococcus pneumoniae">
            <concept code="Strpne" displayName="Streptococcus pneumoniae" />
        </fromConcepts>
    </conceptMapping>
</ns3:conceptDeterminationMethod>

 

ExecutionEngines

ExecutionEngines consists of one or more ExecutionEngine elements.

Code Block
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titleExecutionEngines Example
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<?xml version="1.0" encoding="UTF-8"?>
<rest:executionEngines xsi:schemaLocation="org.opencds.dss.config_rest.v1_0 ../schema/OpenCDSConfigRest.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:rest="org.opencds.dss.config_rest.v1_0">
    <!--include all supported executionEngine package names in this list, along with the operations they support -->
    <executionEngine>
	...
    </executionEngine>
    <executionEngine>
	...
    </executionEngine>
</rest:executionEngines>

ExecutionEngine

The ExecutionEngine metadata contains information about the rules engine adapter that should be used for rule processing.

Code Block
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titleExecutionEngine Example
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<?xml version="1.0" encoding="UTF-8"?>
<rest:executionEngine xsi:schemaLocation="org.opencds.dss.config_rest.v1_0 ../schema/OpenCDSConfigRest.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:rest="org.opencds.dss.config_rest.v1_0">
    <identifier>org.opencds.service.drools.v55.DroolsAdapter</identifier>
    <description>Drools 5.5 based adapter</description>
    <timestamp>2014-04-08T00:00:00</timestamp>
    <userId>Someone</userId>
    <supportedOperation>EVALUATION.EVALUATE</supportedOperation>
    <supportedOperation>EVALUATION.EVALUATE_AT_SPECIFIED_TIME</supportedOperation>
</rest:executionEngine>

 

KnowledgeModules

Code Block
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titleKnowledgeModules Example
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<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<ns3:knowledgeModules xmlns:ns2="org.opencds.dss.config.v1_0" xmlns:ns3="org.opencds.dss.config_rest.v1_0">
    <knowledgeModule>
	...
    </knowledgeModule>
    <knowledgeModule>
	...
    </knowledgeModule>
</ns3:knowledgeModules>

 

KnowledgeModule

 

Code Block
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titleKnowledgeModule Example
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<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<ns3:knowledgeModule xmlns:ns2="org.opencds.dss.config.v1_0" xmlns:ns3="org.opencds.dss.config_rest.v1_0">
    <identifier scopingEntityId="org.opencds" businessId="NQF_0031_v1" version="1.1.1" />
    <status>APPROVED</status>
    <executionEngine>org.opencds.service.drools.v55.DroolsAdapter</executionEngine>
    <semanticSignifierId scopingEntityId="org.opencds.vmr" businessId="VMR" version="1.0" />
    <conceptDeterminationMethods />
    <package>
        <packageType>PKG</packageType>
        <packageId>org.opencds^NQF_0031_v1^1.1.1.pkg</packageId>
        <preload>false</preload>
    </package>
    <primaryProcess></primaryProcess>
    <timestamp>2014-07-30T13:21:46.772-06:00</timestamp>
    <userId>phillip</userId>
</ns3:knowledgeModule>

 

SemanticSignifiers

 

Code Block
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titleSemanticSignifiers Example
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<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<ns3:semanticSignifiers xmlns:ns2="org.opencds.dss.config.v1_0" xmlns:ns3="org.opencds.dss.config_rest.v1_0">
    <semanticSignifier>
	...
    </semanticSignifier>
</ns3:semanticSignifiers>

 

SemanticSignifier

 

Code Block
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titleSemanticSignifier Example
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<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<ns3:semanticSignifier xmlns:ns2="org.opencds.dss.config.v1_0" xmlns:ns3="org.opencds.dss.config_rest.v1_0">
    <identifier scopingEntityId="org.opencds.vmr" businessId="VMR" version="1.0" />
    <name>org.opencds.vmr^VMR^1.0</name>
    <description>org.opencds.vmr^VMR^1.0</description>
    <xsdComputableDefinition>
        <xsdRootGlobalElementName>CDSInput</xsdRootGlobalElementName>
        <xsdURL>org.opencds.vmr.v1_0.schema</xsdURL>
    </xsdComputableDefinition>
    <entryPoint>org.opencds.vmr.v1_0.schema.CDSInput</entryPoint>
    <exitPoint>org.opencds.vmr.v1_0.mappings.out.VMRV10ModelExitPoint</exitPoint>
    <timestamp>2014-07-30T13:21:46.750-06:00</timestamp>
    <userId>Someone</userId>
</ns3:semanticSignifier>

 

Examples

<insert examples refs here>

Backend

The OpenCDS backend is configured using one of three methods: Classpath, Filesystem and BDB.  The choice of configuration strategy is made within the opencds.properties file (see OpenCDS RunTime Installation Guide for details).

Classpath

This configuration option is most useful when initially evaluating OpenCDS.  (As an aside, we also use this option for our continuous builds for functional testing purposes.)

When OpenCDS is configured using the Classpath-based configuration, it will look for the configuration files contained in a .jar file in the main .war file.  The opencds.properties file must contain the following lines to enable this configuration strategy:

Code Block
languagetext
knowledge-repository.type=CLASSPATH
knowledge-repository.path=resources_v1.3

Filesystem

When OpenCDS is configured using the Filesystem-based configuration, it will look for the configuration files in a folder specified by the knowledge-repository-path option in the opencds.properties file.  The opencds.properties file must contain the following lines to enable this configuration strategy:

Code Block
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knowledge-repository.type=SIMPLE_FILE
knowledge-repository.path=<path_to_resources_v1.3>

Examples of "path_to_resources_v1.3" include:

  • C:/opencds-knowledge-repository-data/resources_v1.3
    • (Note the forward-slashes for Windows-based systems)
  • /home/opencds/knowledge-repository-data/resources_v1.3

BDB

 

When OpenCDS is configured using the BDB-based configuration, it will look for configuration in the BDB database in the store folder within the folder specified by the knowledge-repository-path.  The opencds.properties file must contain the following lines to enable this configuration strategy:

 

Code Block
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knowledge-repository.type=STORE
knowledge-repository.path=<path_to_store>

 

If the store folder does not exist, OpenCDS will create it at startup.  Please note, however, as this will be a new store, OpenCDS will contain no configuration at all; the Migration tool or the REST Client (see below for each) may be used to upload the configuration metadata to OpenCDS.

Additionally, the folder specified by knowledge-repository.path will also contain two other folders (in addition to store; also created by OpenCDS if they do not exist):

  • knowledgePackages
  • supportingData

These folders will contain the binary knowledge packages (e.g., from Guvnor), and any supporting data which will be used by OpenCDS (the implementation of which will be implemented at a later date) before passing the data into the inferencing engine.  These files are not stored in BDB in order to keep the database size to a minimum.

 

Security

The backend configuration also requires a security file, which contains the username and passwords for each user and the roles for each... 

REST API

Security

Methods

Configuration API (REST) Version 1.0

REST Client

...

Run-time OS

For initial OpenCDS run-time configuration, please start with the relevant section of the documentation according to the operating system where OpenCDS will be deployed, as there are some differences for Windows and Linux/Mac installations:

The remaining configuration is described below:

Schemas

Configuration Schemas

Backend Configuration of OpenCDS Server

Configuration Backend Tooling

REST Service

PLEASE NOTE: OpenCDS Configuration REST Services should be used while no (DSS) requests are being processed by the system.  Doing otherwise may result in a race condition on the configuration backend, yielding potentially unexpected results.

Security

REST Security

Methods

Configuration API (REST) Version 1.0

Front-end Tooling to Re-configure OpenCDS Server

Use of OpenCDS will normally require posting updates to:

  • install new or updated Knowledge Modules (KMs), and the configuration for the KMs, including any
    • Concept Determination Methods (CDMs),
    • Supporting Data, or
    • Plugins required by the new or updated Knowledge Modules.

These configuration changes can be posted to one or more OpenCDS Servers using the Front-end Tooling, which is currently implemented by a REST client.

REST Client

Configuration Front-end Tooling (REST Client)

Migration from Earlier Versions of OpenCDS Configuration

Configuration Migration