DRAFT

Table of Contents

Overview

This document describes the OpenCDS Configuration for version 1.32.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

REST Schema

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.

This style of configuration may be used via the REST service or may exist on the filesystem (as in the 1.2.x and previous configuration).

An example ConceptDeterminationMethods is shown below:

Code Block

theme	Eclipse
language	xml
title	ConceptDeterminationMethods Example
linenumbers	true

<?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 concept elements within fromConcepts compose the local and standard concepts that may be expected in the vMR data. When processing the vMR, for each of the local concepts found, OpenCDS will add the OpenCDS concept (the toConcept) to the internal fact lists.

Elements are described as follows:

conceptMapping - the element wrapping the overall mapping of local/standard concepts to OpenCDS concepts
toConcept - the OpenCDS concept to which all fromConcepts will map
fromConcepts - the wrapper element for local/standard concepts that are mapped to the OpenCDS concept; contains the codeSystem of the concepts (NOTE: multiple fromConcepts within the conceptMapping are supported, in order to support concepts from any number of codeSystems).
- concept - the local/standard concept, within the codeSystem specified in the fromConcepts element.

This style of configuration may be used via the REST service or may exist on the filesystem (as in the 1.2.x and previous configuration).

An example ConceptDeterminationMethod is shown below:

Code Block

theme	Eclipse
language	xml
title	ConceptDeterminationMethod Example
linenumbers	true

<?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.

This style of configuration may be used via the REST service or may exist on the filesystem (as in the 1.2.x and previous configuration).

Code Block

theme	Eclipse
language	xml
title	ExecutionEngines Example
linenumbers	true

<?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. Elements are as follows:

identifier - the identifier of the ExecutionEngine; this should be the fully-qualified class name of the adapter.
description - a free-form description of the ExecutionEngine
timestamp - the timestamp of metadata creation
userId - the user id of the user who created the metadata
supportedOperation - (may include more than one) describes the types of operations supported by the ExecutionEngine.

This style of configuration may be used via the REST service.

Code Block

theme	Eclipse
language	xml
title	ExecutionEngine Example
linenumbers	true

<?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`

KnowledgeModules consists of one or more KnowledgeModule elements.

This style of configuration may be used via the REST service or may exist on the filesystem (as in the 1.2.x and previous configuration).

Code Block

theme	Eclipse
language	xml
title	KnowledgeModules Example
linenumbers	true

<?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`

The KnowledgeModule element consists of metadata describing the KnowledgeModule. Element descriptions are as follows:

identifier - the identifier of the KnowledgeModule, referenced by CDS requests.
status - the status of the KnowledgeModule
executionEngine - the identifier for the ExecutionEngine, used to cross-reference the ExecutionEngine metadata.
semanticSignifierId - the identifier for the SemanticSignifier, used to cross reference the SemanticSignifier metadata.
conceptDeterminationMethods - (to be used in future implementations) describes which Concept Determination Methods should be used for concept mappings, before the data are processed by the rules engine.
package - the metadata describing the knowledge package containing the rules and other artifacts used by the rules engine.
- packageType - the type of package (E.g., Drools accepts, .pkg, .bpmn2, and .drl).
- packageId - the identifier used by OpenCDS to reference the package on the filesystem.
- preload - indication to OpenCDS whether to preload the knowledge package on startup.
primaryProcess - the process name used by Drools (as specified in the BPMN2 process diagram).
timestamp - the time when the metadata were created.
userId - the user id of the user who created/uploaded the KnowledgeModule.

This style of configuration may be used via the REST service.

Code Block

theme	Eclipse
language	xml
title	KnowledgeModule Example
linenumbers	true

<?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</primaryProcess>
    <timestamp>2014-07-30T13:21:46.772-06:00</timestamp>
    <userId>Someone</userId>
</ns3:knowledgeModule>

`SemanticSignifiers`

SemanticSignifiers consists of one or more SemanticSignifier elements.

This style of configuration may be used via the REST service or may exist on the filesystem (as in the 1.2.x and previous configuration).

Code Block

language	xml
title	SemanticSignifiers Example
linenumbers	true

<?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`

The SemanticSignifier element describes the external model of the vMR data that will enter the system. These elements describe how the system should process the incoming vMR data:

identifier - the identifier of the SemanticSignifier
name - a human-readable name of the identifier (typically a ^-delimited combination of the identifier attributes)
description - free-form description of the SemanticSignifier
xsdComputableDefinition
- xsdRootGlobalElementName - the global element name of the schema
- xsdURL - the pathname of the schema implementation (e.g., the package name of the JAXB classes)
entryPoint - the entry point used by OpenCDS to transform the incoming data into the internal model.
exitPoint - the exit point used by OpenCDS to transform the outgoing data into the external model.
timestamp - the timestamp of creation
userId - the user id of the user who created the metadata instance.

This style of configuration may be used via the REST service.

Code Block

language	xml
title	SemanticSignifier Example
linenumbers	true

<?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>

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

language	text

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

language	text

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

language	text

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

Version	Old Version 9	New Version Current
Changes made by	Phillip Warner	David Shields
Saved on	Aug 02, 2014	Jul 21, 2016

Versions Compared

Key

Overview

What's new?

Schemas

Base Schema

REST Schema

Schema Discussion

`ConceptDeterminationMethods`

`ConceptDeterminationMethod`

`ExecutionEngines`

`ExecutionEngine`

`KnowledgeModules`

`KnowledgeModule`

`SemanticSignifiers`

`SemanticSignifier`

Backend

Classpath

Filesystem

BDB

Security

REST API

Security

Methods

REST Client

Run-time OS

Schemas

Backend Configuration of OpenCDS Server

REST Service

Security

Methods

Front-end Tooling to Re-configure OpenCDS Server

REST Client

Migration from Earlier Versions of OpenCDS Configuration

Content Comparison

Versions Compared

Key

Overview

What's new?

Schemas

Base Schema

REST Schema

Schema Discussion

ConceptDeterminationMethods

ConceptDeterminationMethod

ExecutionEngines

ExecutionEngine

KnowledgeModules

KnowledgeModule

SemanticSignifiers

SemanticSignifier

Backend

Classpath

Filesystem

BDB

Security

REST API

Security

Methods

REST Client

Run-time OS

Schemas

Backend Configuration of OpenCDS Server

REST Service

Security

Methods

Front-end Tooling to Re-configure OpenCDS Server

REST Client

Migration from Earlier Versions of OpenCDS Configuration

`ConceptDeterminationMethods`

`ConceptDeterminationMethod`

`ExecutionEngines`

`ExecutionEngine`

`KnowledgeModules`

`KnowledgeModule`

`SemanticSignifiers`

`SemanticSignifier`