convertpheno

Documentation

Index

• Variables
• func ExtractPhenoFileNames(fileList string) ([]string, error)
• func IsWithdrawnSample(sampleID string) bool
• func RunAllBackendBQ(phenoPaths []string, BQ *WrappedBigQuery) error
• func RunAllBackendCSV(phenoPaths []string, dictionaryCSV string) error
• func SetWithdrawnSamples(withdrawnSampleIDList []string)
• func SetWithdrawnSamplesFromFile(withdrawnSampleFile string) error
• type CodingFileLookup
• type Column
• type SamplePheno
• type WrappedBigQuery

Variables

var (
	BufferSize = 4096 * 8
	STDOUT     = bufio.NewWriterSize(os.Stdout, BufferSize)
)

Functions

func ExtractPhenoFileNames

func ExtractPhenoFileNames(fileList string) ([]string, error)

func IsWithdrawnSample

func IsWithdrawnSample(sampleID string) bool

IsWithdrawnSample returns true if the given sample ID is in the withdrawn sample lookup table.

func RunAllBackendBQ

func RunAllBackendBQ(phenoPaths []string, BQ *WrappedBigQuery) error

func RunAllBackendCSV

func RunAllBackendCSV(phenoPaths []string, dictionaryCSV string) error

func SetWithdrawnSamples

func SetWithdrawnSamples(withdrawnSampleIDList []string)

SetWithdrawnSamples is not safe for concurrent use.

func SetWithdrawnSamplesFromFile

func SetWithdrawnSamplesFromFile(withdrawnSampleFile string) error

SetWithdrawnSamplesFromFile is not safe for concurrent use. It allows you to set the lookup table.

Types

type CodingFileLookup

type CodingFileLookup struct {
	FieldID      int64              `bigquery:"FieldID"`
	CodingFileID bigquery.NullInt64 `bigquery:"coding_file_id"`
}

type Column

type Column struct {
	FieldID      string             `db:"FieldID"`
	Instance     string             `db:"instance"`
	ArrayIDX     string             `db:"array_idx"`
	CodingFileID bigquery.NullInt64 `db:"coding_file_id"`
}

type SamplePheno

type SamplePheno struct {
	Column
	SampleID string `db:"sample_id"`
	Value    string `db:"value"`
}

type WrappedBigQuery

type WrappedBigQuery struct {
	Context  context.Context
	Client   *bigquery.Client
	Project  string
	Database string
}