databio

README

datab.io

Please cite this work as

• Reid RW, Ferrier JW, Jay JJ. Automated gene data integration with Databio. BMC Res Notes. 2020 Apr 1;13(1):195. PMID: 32238171 PMCID: PMC7110638

A web portal that does automated identifier translation for bioinformatics.

Use case

Ever find a dataset that looked amazing? Only problem is that it uses Gene IDs that you aren't familiar with... With https://datab.io you can just upload the data file, it will automatically determine what identifiers are present and what they can be translated into. It'll then do the translation for you and export a ZIP file containing everything you need to include in a publication to ensure data provenance including methodological descriptions with citations, versions and timestamps.

License

GPLv3

Documentation

Index

• Variables
• func CheckDirectories() error
• func GetDownloadPath(filename string) string
• func GetResult(token, resType string, data interface{}) (bool, error)
• func GetResultPath(token string) string
• func GetUploadPath(filename string) string
• func OpenSourceMap(filename string) (*os.File, error)
• func PutResult(token, resType string, data ...interface{}) error

Variables

var (
	// UploadDirectory is the path to place uploaded files.
	UploadDirectory, _ = filepath.Abs("./uploads")

	// ResultDirectory is the path to place result metadata files.
	ResultDirectory, _ = filepath.Abs("./results")

	// DownloadDirectory is the path to place downloadable files.
	DownloadDirectory, _ = filepath.Abs("./downloads")

	// SourceMapsDirectory is the path to source mapping files.
	SourceMapsDirectory, _ = filepath.Abs("./sources")
)

Functions

func CheckDirectories

func CheckDirectories() error

CheckDirectories creates necessary data directories for processing uploads.

func GetDownloadPath

func GetDownloadPath(filename string) string

GetDownloadPath returns the full path and URL to a downloadable file.

func GetResult

func GetResult(token, resType string, data interface{}) (bool, error)

GetResult reads a result from the specified token. Data argument should be a pointer receiver.

func GetResultPath

func GetResultPath(token string) string

GetResultPath returns the full path to a result file.

func GetUploadPath

func GetUploadPath(filename string) string

GetUploadPath returns the full path to an uploaded file.

func OpenSourceMap

func OpenSourceMap(filename string) (*os.File, error)

OpenSourceMap opens a source mapping file and returns it.

func PutResult

func PutResult(token, resType string, data ...interface{}) error

PutResult writes a result to the specified token. Either a single json-serializable data argument can be provided, or multiple interleaved key-value pairs.