database

package
v1.0.6-ti4health Latest Latest
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 Go to latest Published: Jun 29, 2023 License: Apache-2.0 Imports: 11 Imported by: 0

README

Package pkg/datasource/database

This package implements the database access of the data source to its postgresql database.

Documentation

Index

Constants

View Source 
const TestSchemaName = "gecodatasourcetest"

TestSchemaName defines the database schema name used for tests.

Variables

This section is empty.

Functions

This section is empty.

Types

type Events 

type Events struct {
	EventsOfInterest int64
	CensoringEvents  int64
}

Events contains the number of events of interest and censoring events occurring at the same relative time.

type ExploreQuery 

type ExploreQuery struct {
	ID                            string
	CreateDate                    string
	UserID                        string
	Status                        string
	Definition                    string
	ResultI2b2PatientSetID        sql.NullInt64
	ResultGecoSharedIDCount       sql.NullString
	ResultGecoSharedIDPatientList sql.NullString
}

ExploreQuery is an explore query such as stored in the database.

type OntologyElement 

type OntologyElement struct {
	FullName         string
	Name             string
	VisualAttributes string
	BaseCode         string
	MetaDataXML      sql.NullString
	Comment          sql.NullString
	AppliedPath      string
	ID               int
}

OntologyElement is an i2b2 ontology element as stored in the database.

type PostgresDatabase 

type PostgresDatabase struct {
	PostgresDatabaseConfig

	Ctx *context.Context // For telemetry
	// contains filtered or unexported fields
}

PostgresDatabase wraps the Postgres database of the data source.

func NewPostgresDatabase 

func NewPostgresDatabase(ctx *context.Context, logger logrus.FieldLogger, config PostgresDatabaseConfig, dbHandle *sql.DB) (db *PostgresDatabase, err error)

NewPostgresDatabase initializes a connection to a postgres database, and loads its structure if not present.

func (PostgresDatabase) AddCohort 

func (db PostgresDatabase) AddCohort(userID, cohortName, exploreQueryID, projectID string) (err error)

AddCohort adds a saved cohort for a user. Returns an error (due to foreign key violation) if the explore query does not exist, or if the provided user does not match.

func (PostgresDatabase) AddExploreQuery 

func (db PostgresDatabase) AddExploreQuery(userID, queryID, queryDefinition string) (err error)

AddExploreQuery adds an explore query with the requested status.

func (PostgresDatabase) BuildTimePoints 

func (db PostgresDatabase) BuildTimePoints(
	patientSetID int64,
	startConceptCodes []string,
	startModifierCodes []string,
	startEarliest bool,
	endConceptCodes []string,
	endModifierCodes []string,
	endEarliest bool,
	maxLimit int64,
) (
	eventAggregates map[int64]*Events,
	patientsWithStartEvent int64,
	patientsWithoutAnyEndEvent map[int64]struct{},
	err error,
)

BuildTimePoints runs the SQL queries, process their results to build sequential data and aggregate them.

func (PostgresDatabase) DeleteCohort 

func (db PostgresDatabase) DeleteCohort(userID, cohortName, exploreQueryID string) (err error)

DeleteCohort deletes a saved cohort for a user.

func (PostgresDatabase) GetCohort 

func (db PostgresDatabase) GetCohort(userID, exploreQueryID string) (cohort *SavedCohort, err error)

GetCohort retrieves a saved cohort from the database. Returns nil (not an error) if cohort does not exist.

func (PostgresDatabase) GetCohorts 

func (db PostgresDatabase) GetCohorts(userID, projectID string, limit int) (cohorts []SavedCohort, err error)

GetCohorts retrieves the saved cohorts of a user from the database.

func (PostgresDatabase) GetConceptCodes 

func (db PostgresDatabase) GetConceptCodes(path string) ([]string, error)

GetConceptCodes returns all concept codes for a given path and its descendants.

func (PostgresDatabase) GetExploreQuery 

func (db PostgresDatabase) GetExploreQuery(userID, id string) (query *ExploreQuery, err error)

GetExploreQuery retrieves an explore query from the database. Returns nil (not an error) if query does not exist.

func (PostgresDatabase) GetModifierCodes 

func (db PostgresDatabase) GetModifierCodes(path string, appliedPath string) ([]string, error)

GetModifierCodes returns all modifier codes for a given path and its descendants, and exactly matching the appliedPath.

func (PostgresDatabase) RetrieveObservationsForConcept 

func (db PostgresDatabase) RetrieveObservationsForConcept(code string, patientSetID, minObservations int64) (statsObservations []StatsObservation, err error)

RetrieveObservationsForConcept returns the numerical values that correspond to the concept passed as argument for the specified cohort.

func (PostgresDatabase) RetrieveObservationsForModifier 

func (db PostgresDatabase) RetrieveObservationsForModifier(code string, patientSetID, minObservations int64) (statsObservations []StatsObservation, err error)

RetrieveObservationsForModifier returns the numerical values that correspond to the modifier passed as argument for the specified cohort.

func (PostgresDatabase) SearchOntology 

func (db PostgresDatabase) SearchOntology(searchString, limit string) (ontologyElements []OntologyElement, err error)

SearchOntology retrieves the elements (both concepts and modifiers, at most @limit, default 10) of the ontology whose names contains @searchString.

func (PostgresDatabase) SetExploreQueryError 

func (db PostgresDatabase) SetExploreQueryError(userID, queryID string) error

SetExploreQueryError sets the error status to an explore query.

func (PostgresDatabase) SetExploreQueryRunning 

func (db PostgresDatabase) SetExploreQueryRunning(userID, queryID string) error

SetExploreQueryRunning sets the running status to an explore query.

func (PostgresDatabase) SetExploreQuerySuccess 

func (db PostgresDatabase) SetExploreQuerySuccess(userID, queryID, i2b2PatientSetID, gecoSharedIDCount, gecoSharedIDPatientList string) error

SetExploreQuerySuccess sets the success status to an explore query and stores its results.

func (PostgresDatabase) TestCleanUp 

func (db PostgresDatabase) TestCleanUp() error

TestCleanUp deletes ALL test data and structure of the data source. Use with caution!

func (PostgresDatabase) TestLoadData 

func (db PostgresDatabase) TestLoadData() error

TestLoadData loads test data into the database. For usage with tests.

type PostgresDatabaseConfig 

type PostgresDatabaseConfig struct {
	Host     string
	Port     string
	Database string
	Schema   string
	User     string
	Password string
}

PostgresDatabaseConfig is the config used to connect to the postgres database

func (PostgresDatabaseConfig) DataSourceName 

func (conf PostgresDatabaseConfig) DataSourceName() string

DataSourceName should return the connection string to the db: postgres example "host=localhost port=5432 user=test password=test dbname=test sslmode=disable"

func (PostgresDatabaseConfig) Driver 

func (conf PostgresDatabaseConfig) Driver() driver.Driver

Driver Should return the database driver

func (PostgresDatabaseConfig) DriverName 

func (conf PostgresDatabaseConfig) DriverName() string

DriverName returns "postgres"

func (PostgresDatabaseConfig) Name 

func (conf PostgresDatabaseConfig) Name() string

Name should return the name of the connected database

type SavedCohort 

type SavedCohort struct {
	Name         string
	ProjectID    string
	CreateDate   string
	ExploreQuery ExploreQuery
}

SavedCohort is a cohort such as stored in the database.

type StatsObservation 

type StatsObservation struct {
	NumericValue  float64
	Unit          string
	PatientNumber int64
}

StatsObservation contains a patient observation.

Source Files

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