Package org.odpi.openmetadata.samples.governanceactions.clinicaltrials

Class CocoClinicalTrialBaseService

java.lang.Object

org.odpi.openmetadata.frameworks.connectors.Connector

org.odpi.openmetadata.frameworks.connectors.ConnectorBase

org.odpi.openmetadata.frameworks.opengovernance.GovernanceActionServiceConnector

org.odpi.openmetadata.frameworks.opengovernance.GeneralGovernanceActionService

org.odpi.openmetadata.samples.governanceactions.clinicaltrials.CocoClinicalTrialBaseService

All Implemented Interfaces:

AuditLoggingComponent, SecureConnectorExtension, VirtualConnectorExtension, GovernanceActionService

Direct Known Subclasses:

CocoClinicalTrialCertifyHospitalService, CocoClinicalTrialHospitalOnboardingService, CocoClinicalTrialNominateHospitalService, CocoClinicalTrialSetUpDataLakeService, CocoClinicalTrialSetUpService

public class CocoClinicalTrialBaseService
extends GeneralGovernanceActionService

Provides shared functions for the clinical trial services.

The services are written to be re-runnable: if a run fails part way through, or a clinical trial is set up a second time, each element and relationship that the earlier run created is found and reused rather than created again. Without this, the second run fails on the first element it tries to create, since its qualified name is already taken (OMAG-COMMON-409-001), and the elements the earlier run left behind have to be removed by hand before the service can be run again. The find-or-create methods below provide this behaviour.

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
protected static class	CocoClinicalTrialBaseService.PersonContactDetails

Nested classes/interfaces inherited from class org.odpi.openmetadata.frameworks.connectors.ConnectorBase

ConnectorBase.ProtectedConnection

Field Summary

Fields inherited from class org.odpi.openmetadata.frameworks.opengovernance.GeneralGovernanceActionService

governanceContext

Fields inherited from class org.odpi.openmetadata.frameworks.opengovernance.GovernanceActionServiceConnector

governanceServiceName, propertyHelper

Fields inherited from class org.odpi.openmetadata.frameworks.connectors.ConnectorBase

auditLog, connectionBean, connectorInstanceId, embeddedConnectors, messageFormatter, secretsStoreConnectorMap

Constructor Summary

Constructors

Constructor	Description
CocoClinicalTrialBaseService()

Method Summary

Modifier and Type	Method	Description
protected void	addActionTargetToProcess(String processGUID, String actionTargetName, String actionTargetGUID)	Link an action target to a process.
protected void	addGovernedByRelationship(String dataQualityCertificationTypeGUID, String sandboxSchemaGUID)	Link the certification type to the schema.
protected void	addResourceListRelationship(String consumerGUID, String resourceGUID, ResourceUse resourceUse)	Set up the ResourceList relationship between an implementation component and a solution component.
protected void	addSolutionComponentImplementationResource(String solutionComponentGUID, String implementationGUID, String role, String description)	Set up the ImplementedBy relationship between an implementation component and a solution component.
protected void	addSolutionComponentImplementedByRelationship(String solutionComponentGUID, String implementationGUID, String informationSupplyChainQualifiedName, String role)	Set up the ImplementedBy relationship between an implementation component and a solution component.
protected void	checkCertificationValidForProject(String projectGUID, String certificationTypeGUID)	Check that the certification type is associated with the requested project.
protected String	createLineageRelationshipIfAbsent(String relationshipName, String sourceElementGUID, String iscQualifiedName, String label, String description, String formula, String formulaType, String queryId, String query, String guard, String lineNumber, String targetElementGUID)	Create a lineage relationship unless an identical one is already in place.
protected String	createPopulateSandboxDAG(String airflowDAGName, String topLevelProjectGUID)	Create a process to represent the Airflow DAG that populates the sandbox.
protected String	createProcessFromGovernanceActionTypeIfAbsent(String processType, String processQualifiedName, String processName, String processDescription, int domainIdentifier, String governanceActionTypeGUID, Map<String,String> additionalRequestParameters, String anchorGUID, List<String> anchorScopeGUIDs)	Create a specific governance action process from a generic governance action type, unless a process with this qualified name already exists.
protected String	createRelationshipIfAbsent(String relationshipTypeName, String end1GUID, String end2GUID, ElementProperties properties)	Create a relationship unless an identical one is already in place.
protected String	createSandboxSchema(String topLevelProjectGUID)	Create the sandbox database schema - it is assumed that details of the schema are passed in the request parameters.
protected CocoClinicalTrialBaseService.PersonContactDetails	getContactDetailsForPersonGUID(String personGUID)	Retrieve the email for a specific person.
protected String	getElementGUIDByQualifiedName(String qualifiedName)	Return the unique identifier of the element with this qualified name, or null if there is none.
protected String	getExistingElementGUID(ElementProperties properties)	Return the unique identifier of the element that would be created with these properties, if it already exists.
protected String	getExistingRelationshipGUID(String relationshipTypeName, String end1GUID, String end2GUID, ElementProperties properties)	Return the unique identifier of the relationship of this type from end1 to end2 whose properties include all the supplied string properties, or null if there is none.
protected String	getExistingTemplatedElementGUID(String templateGUID, ElementProperties replacementProperties, Map<String,String> placeholderProperties)	Return the unique identifier of the element that a template would create, if it already exists.
protected String	getInformationSupplyChainQualifiedName(String informationSupplyChainGUID)	Extract the qualified name for the information supply chain.
protected NewElementProperties	getResourceUseProperties(ResourceUse resourceUse)	Set up the properties for a resource use enum.
protected boolean	isClassified(String elementGUID, String classificationName)	Return whether the element already has the named classification.

Methods inherited from class org.odpi.openmetadata.frameworks.opengovernance.GeneralGovernanceActionService

disconnect, getActionTarget, getAllActionTargets, getProperty, setGovernanceContext, start

Methods inherited from class org.odpi.openmetadata.frameworks.opengovernance.GovernanceActionServiceConnector

getArrayRequestParameter, getBooleanRequestParameter, getConnectorComponentDescription, getIntRequestParameter, getLongRequestParameter, getStringRequestParameter, handleUnexpectedException, setAuditLog, setGovernanceServiceName, validateContext

Methods inherited from class org.odpi.openmetadata.frameworks.connectors.ConnectorBase

combineConfigurationProperties, disconnectConnectors, equals, fromCamelToCanonicalCase, fromCanonicalToCamelCase, fromCanonicalToKebabCase, fromCanonicalToSnakeCase, fromKebabToCanonicalCase, fromSnakeToCanonicalCase, getArrayConfigurationProperty, getArrayConfigurationProperty, getArrayConfigurationProperty, getArrayValue, getBooleanConfigurationProperty, getConnection, getConnectorInstanceId, getDateConfigurationProperty, getIntConfigurationProperty, getLongConfigurationProperty, getSecretsCollectionName, getSecretsLocation, getSecretsProvider, getStringConfigurationProperty, getStringConfigurationProperty, getSuppliedPlaceholderProperties, hashCode, initialize, initializeEmbeddedConnectors, initializeSecretsStoreConnector, isActive, logExceptionRecord, logExceptionRecord, logRecord, logRecord, throwMissingConfigurationProperty, throwMissingElement, throwMissingEndpointAddress, throwMissingResource, throwNoAsset, throwWrongTypeOfAsset, throwWrongTypeOfResource, throwWrongTypeOfRootSchema, toString

Methods inherited from class org.odpi.openmetadata.frameworks.connectors.Connector

clearStatisticProperty, clearStatisticTimestamp, getConnectorStatistics, getStatisticCounter, getStatisticProperty, getStatisticTimestamp, incrementStatisticCounter, initializeStatisticCounter, refreshStatistics, setStatisticProperty, setStatisticTimestamp

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Details

CocoClinicalTrialBaseService

public CocoClinicalTrialBaseService()

Method Details

getElementGUIDByQualifiedName

protected String getElementGUIDByQualifiedName(String qualifiedName)
                                        throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Return the unique identifier of the element with this qualified name, or null if there is none.

Parameters:

qualifiedName - qualified name to look for

Returns:

unique identifier or null

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - problem accessing the metadata repository/server

UserNotAuthorizedException - security problem

getExistingElementGUID

protected String getExistingElementGUID(ElementProperties properties)
                                 throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Return the unique identifier of the element that would be created with these properties, if it already exists.

Parameters:

properties - properties of the new element, which include its qualified name

Returns:

unique identifier or null

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - problem accessing the metadata repository/server

UserNotAuthorizedException - security problem

getExistingTemplatedElementGUID

protected String getExistingTemplatedElementGUID(String templateGUID,
 ElementProperties replacementProperties,
 Map<String,String> placeholderProperties)
                                          throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Return the unique identifier of the element that a template would create, if it already exists. The new element's qualified name comes from the replacement properties if they set one, and from the template otherwise, with the placeholders filled in the same way the template is copied. If a placeholder is left unfilled, the name cannot be predicted, and null is returned so that the element is created.

Parameters:

templateGUID - unique identifier of the template

replacementProperties - properties that override the template's (may be null)

placeholderProperties - placeholder values (may be null)

Returns:

unique identifier or null

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - problem accessing the metadata repository/server

UserNotAuthorizedException - security problem

getExistingRelationshipGUID

protected String getExistingRelationshipGUID(String relationshipTypeName,
 String end1GUID,
 String end2GUID,
 ElementProperties properties)
                                      throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Return the unique identifier of the relationship of this type from end1 to end2 whose properties include all the supplied string properties, or null if there is none. Matching on the properties as well as the ends keeps apart relationships that are legitimately repeated between the same two elements - an action target under two different names, a person assigned to a project in two roles, or lineage for two information supply chains.

Parameters:

relationshipTypeName - type of relationship

end1GUID - unique identifier of the element at end 1

end2GUID - unique identifier of the element at end 2

properties - properties of the new relationship (may be null)

Returns:

unique identifier of the relationship or null

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - problem accessing the metadata repository/server

UserNotAuthorizedException - security problem

createRelationshipIfAbsent

protected String createRelationshipIfAbsent(String relationshipTypeName,
 String end1GUID,
 String end2GUID,
 ElementProperties properties)
                                     throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Create a relationship unless an identical one is already in place.

Parameters:

relationshipTypeName - type of relationship

end1GUID - unique identifier of the element at end 1

end2GUID - unique identifier of the element at end 2

properties - properties of the relationship (may be null)

Returns:

unique identifier of the new or existing relationship

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - problem accessing the metadata repository/server

UserNotAuthorizedException - security problem

createLineageRelationshipIfAbsent

protected String createLineageRelationshipIfAbsent(String relationshipName,
 String sourceElementGUID,
 String iscQualifiedName,
 String label,
 String description,
 String formula,
 String formulaType,
 String queryId,
 String query,
 String guard,
 String lineNumber,
 String targetElementGUID)
                                            throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Create a lineage relationship unless an identical one is already in place. The parameters are those of GovernanceActionContext.createLineageRelationship.

Parameters:

relationshipName - either LineageMapping, ProcessCall, DataFlow, ControlFlow.

sourceElementGUID - unique identifier of the element that describes the source of the data.

iscQualifiedName - qualifiedName of the information supply chain

label - label for when the lineage relationship is visualized

description - description of the lineage relationship

formula - expression summary

formulaType - language used to express the formula

queryId - identifier for the process query - DataMapping Relationship

query - the process query - DataMapping Relationship

guard - value that indicated a control path to take - ControlFlow relationship

lineNumber - line number where the call is made - ProcessCall Relationship

targetElementGUID - unique identifier of the element that describes the destination of the data.

Returns:

unique identifier of the new or existing relationship

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - problem accessing the metadata repository/server

UserNotAuthorizedException - security problem

isClassified

protected boolean isClassified(String elementGUID,
 String classificationName)
                        throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Return whether the element already has the named classification.

Parameters:

elementGUID - unique identifier of the element

classificationName - name of the classification

Returns:

flag

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - problem accessing the metadata repository/server

UserNotAuthorizedException - security problem

createProcessFromGovernanceActionTypeIfAbsent

protected String createProcessFromGovernanceActionTypeIfAbsent(String processType,
 String processQualifiedName,
 String processName,
 String processDescription,
 int domainIdentifier,
 String governanceActionTypeGUID,
 Map<String,String> additionalRequestParameters,
 String anchorGUID,
 List<String> anchorScopeGUIDs)
                                                        throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Create a specific governance action process from a generic governance action type, unless a process with this qualified name already exists. The parameters are those of createProcessFromGovernanceActionType.

Parameters:

processType - type of the process

processQualifiedName - new qualified name for the process

processName - new name for the process

processDescription - new description for the process

domainIdentifier - governance domain

governanceActionTypeGUID - the unique identifier of the governance action type

additionalRequestParameters - the additional, predefined request parameters to add to the GovernanceActionProcessFlow relationship

anchorGUID - unique identifier of the anchor

anchorScopeGUIDs - unique identifier for the top level project - used as a search scope

Returns:

unique identifier of the new or existing governance action process

Throws:

InvalidParameterException - parameter error

PropertyServerException - repository error

UserNotAuthorizedException - authorization error

getInformationSupplyChainQualifiedName

protected String getInformationSupplyChainQualifiedName(String informationSupplyChainGUID)
                                                 throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Extract the qualified name for the information supply chain.

Parameters:

informationSupplyChainGUID - unique identifier of the information supply chain element

Returns:

string

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - problem accessing the metadata repository/server

UserNotAuthorizedException - security problem

getContactDetailsForPersonGUID

protected CocoClinicalTrialBaseService.PersonContactDetails getContactDetailsForPersonGUID(String personGUID)
                                                                                    throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Retrieve the email for a specific person.

Parameters:

personGUID - unique identifier of the person entity for the individual

Returns:

email address for the individual; or null if it is not found

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - problem accessing the metadata repository/server

UserNotAuthorizedException - security problem

checkCertificationValidForProject

protected void checkCertificationValidForProject(String projectGUID,
 String certificationTypeGUID)
                                          throws ConnectorCheckedException,
InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Check that the certification type is associated with the requested project. Otherwise, the certification does not make sense.

Parameters:

projectGUID - unique identifier of the project

certificationTypeGUID - unique identifier of the certification type

Throws:

ConnectorCheckedException - the certification type is not linked to the project

InvalidParameterException - invalid parameter passed somehow

PropertyServerException - problem connecting to the open metadata repository

UserNotAuthorizedException - security problem

addActionTargetToProcess

protected void addActionTargetToProcess(String processGUID,
 String actionTargetName,
 String actionTargetGUID)
                                 throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Link an action target to a process. This action target will be available for all steps in the process.

Parameters:

processGUID - unique identifier of the process

actionTargetName - name of the target for action relationship

actionTargetGUID - unique identifier of the target

Throws:

InvalidParameterException - parameter error

PropertyServerException - repository error

UserNotAuthorizedException - authorization error

addSolutionComponentImplementedByRelationship

protected void addSolutionComponentImplementedByRelationship(String solutionComponentGUID,
 String implementationGUID,
 String informationSupplyChainQualifiedName,
 String role)
                                                      throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Set up the ImplementedBy relationship between an implementation component and a solution component. The information supply chain qualified names ensures that the appropriate assets are returned on a specific ISC lineage query.

Parameters:

solutionComponentGUID - unique identifier of the solution component

implementationGUID - unique identifier of the newly set up governance action process

informationSupplyChainQualifiedName - option name of information supply chain - used to identify solution component implementations that are specific to a particular information supply chain

role - optional role of the implementation

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - repository error

UserNotAuthorizedException - security error

addSolutionComponentImplementationResource

protected void addSolutionComponentImplementationResource(String solutionComponentGUID,
 String implementationGUID,
 String role,
 String description)
                                                   throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Set up the ImplementedBy relationship between an implementation component and a solution component. The information supply chain qualified names ensures that the appropriate assets are returned on a specific ISC lineage query.

Parameters:

solutionComponentGUID - unique identifier of the solution component

implementationGUID - unique identifier of the newly set up governance action process

role - role of the component in an implementation

description - optional description of the implementation

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - repository error

UserNotAuthorizedException - security error

addResourceListRelationship

protected void addResourceListRelationship(String consumerGUID,
 String resourceGUID,
 ResourceUse resourceUse)
                                    throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Set up the ResourceList relationship between an implementation component and a solution component.

Parameters:

consumerGUID - unique identifier of the element that is to use the element

resourceGUID - unique identifier of the resource

resourceUse - how is the resource to be used?

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - repository error

UserNotAuthorizedException - security error

getResourceUseProperties

protected NewElementProperties getResourceUseProperties(ResourceUse resourceUse)

Set up the properties for a resource use enum.

Parameters:

resourceUse - enum

Returns:

element properties

addGovernedByRelationship

protected void addGovernedByRelationship(String dataQualityCertificationTypeGUID,
 String sandboxSchemaGUID)
                                  throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Link the certification type to the schema.

Parameters:

dataQualityCertificationTypeGUID - certification type

sandboxSchemaGUID - database schema for the sandbox

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - repository error

UserNotAuthorizedException - security error

createPopulateSandboxDAG

protected String createPopulateSandboxDAG(String airflowDAGName,
 String topLevelProjectGUID)
                                   throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Create a process to represent the Airflow DAG that populates the sandbox.

Parameters:

airflowDAGName - name

topLevelProjectGUID - unique identifier for the top level project - used as a search scope

Returns:

guid

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - repository error

UserNotAuthorizedException - security error

createSandboxSchema

protected String createSandboxSchema(String topLevelProjectGUID)
                              throws InvalidParameterException,
PropertyServerException,
UserNotAuthorizedException

Create the sandbox database schema - it is assumed that details of the schema are passed in the request parameters.

Parameters:

topLevelProjectGUID - unique identifier for the top level project - used as a search scope

Returns:

guid

Throws:

InvalidParameterException - invalid parameter

PropertyServerException - repository error

UserNotAuthorizedException - security error