datasource

package
v1.0.6-ti4health Latest Latest
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 Go to latest Published: Jun 29, 2023 License: Apache-2.0 Imports: 20 Imported by: 0

README

Package pkg/datasource

This package exposes the i2b2 data source conforming to the TI Note data source plugin interface. It implements the different operations of the i2b2 data source.

Documentation

Index

Constants

View Source 
const (
	// DataSourceType is the type of the data source.
	DataSourceType sdk.DataSourceType = "i2b2"

	// DBCredentialsID is the ID for the database credentials.
	DBCredentialsID string = "dbCredentials"
	// I2B2CredentialsID is the ID for the i2b2 credentials.
	I2B2CredentialsID string = "i2b2Credentials"
)

Variables

This section is empty.

Functions

func NewI2b2DataSource 

func NewI2b2DataSource(dsc *sdk.DataSourceCore, config map[string]interface{}, manager *sdk.DBManager) (plugin sdk.DataSource, err error)

NewI2b2DataSource creates an i2b2 data source. It implements sdk.DataSourceFactory.

Types

type I2b2DataSource 

type I2b2DataSource struct {
	sdk.DataSourceCore
	// contains filtered or unexported fields
}

I2b2DataSource is an i2b2 data source for the TI Note. It implements the data source interface.

func (*I2b2DataSource) AddCohort 

func (ds *I2b2DataSource) AddCohort(userID string, params *models.AddDeleteCohortParameters) error

AddCohort adds a cohort.

func (*I2b2DataSource) AddCohortHandler 

func (ds *I2b2DataSource) AddCohortHandler(userID string, jsonParameters []byte, _ map[gecosdk.OutputDataObjectName]gecomodels.DataObjectSharedID) (_ []byte, _ []gecosdk.DataObject, err error)

AddCohortHandler is the OperationHandler for the addCohort Operation.

func (*I2b2DataSource) Close 

func (ds *I2b2DataSource) Close() (err error)

Close closes the i2b2 datasource

func (*I2b2DataSource) Config 

func (ds *I2b2DataSource) Config(logger logrus.FieldLogger, config map[string]interface{}) (err error)

Config configures the datasource. Configuration keys: - I2b2: i2b2.api.url, i2b2.api.domain, i2b2.api.project, i2b2.api.wait-time, i2b2.api.ont-max-elements - Database: db.host, db.port, db.db-name, db.schema-name

func (*I2b2DataSource) ConfigFromDB 

func (ds *I2b2DataSource) ConfigFromDB(logger logrus.FieldLogger) (err error)

ConfigFromDB configures the data source retrieved from the DB.

func (*I2b2DataSource) Data 

func (ds *I2b2DataSource) Data() map[string]interface{}

Data returns all the data to be stored in the TI Note object storage.

func (*I2b2DataSource) DeleteCohort 

func (ds *I2b2DataSource) DeleteCohort(userID string, params *models.AddDeleteCohortParameters) error

DeleteCohort deletes a cohort.

func (*I2b2DataSource) DeleteCohortHandler 

func (ds *I2b2DataSource) DeleteCohortHandler(userID string, jsonParameters []byte, _ map[gecosdk.OutputDataObjectName]gecomodels.DataObjectSharedID) (_ []byte, _ []gecosdk.DataObject, err error)

DeleteCohortHandler is the OperationHandler for the deleteCohort Operation.

func (*I2b2DataSource) ExploreQuery 

func (ds *I2b2DataSource) ExploreQuery(userID string, params *models.ExploreQueryParameters) (patientSetID string, patientCount int64, err error)

ExploreQuery makes an explore query, i.e. an i2b2 CRC (PSM) query.

func (*I2b2DataSource) ExploreQueryHandler 

func (ds *I2b2DataSource) ExploreQueryHandler(userID string, jsonParameters []byte, outputDataObjectsSharedIDs map[gecosdk.OutputDataObjectName]gecomodels.DataObjectSharedID) (jsonResults []byte, outputDataObjects []gecosdk.DataObject, err error)

ExploreQueryHandler is the OperationHandler for the OperationExploreQuery Operation.

func (*I2b2DataSource) GetCohorts 

func (ds *I2b2DataSource) GetCohorts(userID string, params *models.GetCohortsParameters) (results *models.CohortResults, err error)

GetCohorts retrieves the list of cohorts of the user.

func (*I2b2DataSource) GetCohortsHandler 

func (ds *I2b2DataSource) GetCohortsHandler(userID string, jsonParameters []byte, _ map[gecosdk.OutputDataObjectName]gecomodels.DataObjectSharedID) (jsonResults []byte, _ []gecosdk.DataObject, err error)

GetCohortsHandler is the OperationHandler for the getCohorts Operation.

func (*I2b2DataSource) GetContext 

func (ds *I2b2DataSource) GetContext() *context.Context

GetContext return of context of the data source

func (*I2b2DataSource) GetDataSourceConfig 

func (ds *I2b2DataSource) GetDataSourceConfig() map[string]interface{}

GetDataSourceConfig gets the data source config.

func (*I2b2DataSource) GetDataSourceCustomData 

func (ds *I2b2DataSource) GetDataSourceCustomData() map[string]interface{}

GetDataSourceCustomData returns a map of the data values stored along this data source

func (*I2b2DataSource) Query 

func (ds *I2b2DataSource) Query(userID string, params map[string]interface{}, resultKeys ...string) (map[string]interface{}, error)

Query implements the data source interface Query function.

func (*I2b2DataSource) SearchConcept 

func (ds *I2b2DataSource) SearchConcept(params *models.SearchConceptParameters) (*models.SearchResult, error)

SearchConcept retrieves the info about or the children of the concept identified by the params.

func (*I2b2DataSource) SearchConceptHandler 

func (ds *I2b2DataSource) SearchConceptHandler(_ string, jsonParameters []byte, _ map[gecosdk.OutputDataObjectName]gecomodels.DataObjectSharedID) (jsonResults []byte, _ []gecosdk.DataObject, err error)

SearchConceptHandler is the OperationHandler for the OperationSearchConcept Operation.

func (*I2b2DataSource) SearchModifier 

func (ds *I2b2DataSource) SearchModifier(params *models.SearchModifierParameters) (*models.SearchResult, error)

SearchModifier retrieves the info about or the children of the modifier identified by params.

func (*I2b2DataSource) SearchModifierHandler 

func (ds *I2b2DataSource) SearchModifierHandler(_ string, jsonParameters []byte, _ map[gecosdk.OutputDataObjectName]gecomodels.DataObjectSharedID) (jsonResults []byte, _ []gecosdk.DataObject, err error)

SearchModifierHandler is the OperationHandler for the OperationSearchModifier Operation.

func (*I2b2DataSource) SearchOntology 

func (ds *I2b2DataSource) SearchOntology(params *models.SearchOntologyParameters) (*models.SearchResult, error)

SearchOntology retrieves the info about the concepts and modifiers identified by params.

func (*I2b2DataSource) SearchOntologyHandler 

func (ds *I2b2DataSource) SearchOntologyHandler(_ string, jsonParameters []byte, _ map[gecosdk.OutputDataObjectName]gecomodels.DataObjectSharedID) (jsonResults []byte, _ []gecosdk.DataObject, err error)

SearchOntologyHandler is the OperationHandler for the OperationSearchOntology Operation.

func (*I2b2DataSource) SetContext 

func (ds *I2b2DataSource) SetContext(ctx *context.Context)

SetContext sets a context of the data source

func (*I2b2DataSource) SetDataSourceConfig 

func (ds *I2b2DataSource) SetDataSourceConfig(config map[string]interface{}) error

SetDataSourceConfig sets the data source config.

func (*I2b2DataSource) StatisticsQuery 

func (ds *I2b2DataSource) StatisticsQuery(userID string, params *models.StatisticsQueryParameters) (statResults []*models.StatsResult, err error)

StatisticsQuery makes a statistics query.

func (*I2b2DataSource) StatisticsQueryHandler 

func (ds *I2b2DataSource) StatisticsQueryHandler(
	userID string,
	jsonParameters []byte,
	outputDataObjectsSharedIDs map[gecosdk.OutputDataObjectName]gecomodels.DataObjectSharedID,
) (jsonResults []byte, outputDataObjects []gecosdk.DataObject, err error)

StatisticsQueryHandler is the OperationHandler for the OperationStatisticsQuery Operation.

func (*I2b2DataSource) StatisticsQueryThroughPDOQuery 

func (ds *I2b2DataSource) StatisticsQueryThroughPDOQuery(userID string, params *models.StatisticsQueryParameters) (statResults []*i2b2clientmodels.StatsResult, err error)

StatisticsQueryThroughPDOQuery makes a statistics query retrieves the observation through an i2b2 PDO query. It works (it should be better tested though) but it is not used at the moment because it takes much longer than the version that access the database directly.

func (*I2b2DataSource) SurvivalQuery 

func (ds *I2b2DataSource) SurvivalQuery(userID string, params *models.SurvivalQueryParameters) (survivalQueryResult []int64, err error)

SurvivalQuery makes a survival query. The returned @survivalQuery result is a slice containing the sorted and flattened EventGroups.

func (*I2b2DataSource) SurvivalQueryHandler 

func (ds *I2b2DataSource) SurvivalQueryHandler(userID string, jsonParameters []byte, outputDataObjectsSharedIDs map[gecosdk.OutputDataObjectName]gecomodels.DataObjectSharedID) (jsonResults []byte, outputDataObjects []gecosdk.DataObject, err error)

SurvivalQueryHandler is the OperationHandler for the OperationSurvivalQuery Operation.

type Operation 

type Operation string

Operation is an operation of the data source supported by I2b2DataSource.Query. 

const (
	OperationSearchConcept   Operation = "searchConcept"
	OperationSearchModifier  Operation = "searchModifier"
	OperationSearchOntology  Operation = "searchOntology"
	OperationExploreQuery    Operation = "exploreQuery"
	OperationGetCohorts      Operation = "getCohorts"
	OperationAddCohort       Operation = "addCohort"
	OperationDeleteCohort    Operation = "deleteCohort"
	OperationSurvivalQuery   Operation = "survivalQuery"
	OperationStatisticsQuery Operation = "statisticsQuery"
)

Enumerated values for Operation.

type OperationHandler 

type OperationHandler func(
	userID string, jsonParameters []byte, outputDataObjectsSharedIDs map[gecosdk.OutputDataObjectName]gecomodels.DataObjectSharedID,
) (
	jsonResults []byte, outputDataObjects []gecosdk.DataObject, err error,
)

OperationHandler is a handler function for an operation of the data source supported by I2b2DataSource.Query.

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