FlowG: Seamless Lab Data Integration

FlowG is a Go package that facilitates the connection between data files from lab equipment and GLIMS, a Laboratory Information System developed by CliniSys. It streamlines common FlowG-related tasks by automatically monitoring lab equipment upload folders and converting data into the FlowG file format.

For detailed documentation, visit pkg.go.dev.

Key Features

• Folder Monitoring: Automatically monitors lab equipment upload directories for new data files.
• FlowG File Generation: Converts lab data into FlowG-compatible files for GLIMS integration.
• Error Handling and Logging: Provides configurable directories for processed data, error handling, and log management.

Installation

To use FlowG in your Go project, import the package in your source code:

import "github.com/bas-dehaan/FlowG"

Configuration

FlowG requires some initial configuration to set up folder paths and logging preferences. Use the SetConfig function to define these parameters.

Configuration Parameters

• glimsDir: The directory where lab equipment uploads new data files.
• processedDir: The directory to store successfully processed data files for archival purposes.
• errorDir: The directory to move files that fail to process correctly.
• logDir: The directory for storing log files.
• logLvl: The log level to control the verbosity of log messages. Options include DEBUG, INFO, WARNING, ERROR, and CRITICAL.

Watching for New Files

Once configuration is complete, use the FileWatch() function to monitor the glimsDir for new files. When a new file is detected, FlowG will call your custom processing function.

Processing Function

Your processing function should load all data into a slice of SampleStruct. Then, you can call GlimsOutput() to generate the FlowG file

Example implementation

package main

import (
    "github.com/bas-dehaan/FlowG"
    "path/filepath"
)

func main() {
    err := FlowG.SetConfig("glimsDir", "path/to/upload/folder")
    err = FlowG.SetConfig("processedDir", "processed/data/archival")
    err = FlowG.SetConfig("errorDir", "data/failed/to/process")
    err = FlowG.SetConfig("logDir", "log/storage/folder")
    err = FlowG.SetConfig("logLvl", FlowG.WARNING)
    if err != nil {
        panic(err)
    }
    
    FlowG.FileWatch(yourProcessingFunction)
}

func yourProcessingFunction(filePath string) bool {
    var samples []FlowG.SampleStruct
    filename := filepath.Base(filePath)
    
    // Your file processing, specific to your input filetype...
    
    ok := FlowG.GlimsOutput(filename, samples)
    return ok
}

Documentation

For more detailed usage instructions, please visit the pkg.go.dev documentation.