// Copyright (C) The Lightning Authors. All rights reserved.
//
// SPDX-License-Identifier: AGPL-3.0

package lightning

import (
	"context"
	"flag"
	"fmt"
	"io"
	"net/http"
	_ "net/http/pprof"

	"git.arvados.org/arvados.git/sdk/go/arvados"
	log "github.com/sirupsen/logrus"
)

type flakecmd struct {
	filter filter
}

func (cmd *flakecmd) RunCommand(prog string, args []string, stdin io.Reader, stdout, stderr io.Writer) int {
	var err error
	defer func() {
		if err != nil {
			fmt.Fprintf(stderr, "%s\n", err)
		}
	}()
	flags := flag.NewFlagSet("", flag.ContinueOnError)
	flags.SetOutput(stderr)
	pprof := flags.String("pprof", "", "serve Go profile data at http://`[addr]:port`")
	runlocal := flags.Bool("local", false, "run on local host (default: run in an arvados container)")
	projectUUID := flags.String("project", "", "project `UUID` for output data")
	priority := flags.Int("priority", 500, "container request priority")
	inputDir := flags.String("input-dir", "./in", "input `directory`")
	outputDir := flags.String("output-dir", "./out", "output `directory`")
	cmd.filter.Flags(flags)
	err = flags.Parse(args)
	if err == flag.ErrHelp {
		err = nil
		return 0
	} else if err != nil {
		return 2
	} else if flags.NArg() > 0 {
		err = fmt.Errorf("errant command line arguments after parsed flags: %v", flags.Args())
		return 2
	}

	if *pprof != "" {
		go func() {
			log.Println(http.ListenAndServe(*pprof, nil))
		}()
	}

	if !*runlocal {
		runner := arvadosContainerRunner{
			Name:        "lightning flake",
			Client:      arvados.NewClientFromEnv(),
			ProjectUUID: *projectUUID,
			RAM:         700000000000,
			VCPUs:       96,
			Priority:    *priority,
			KeepCache:   2,
			APIAccess:   true,
		}
		err = runner.TranslatePaths(inputDir)
		if err != nil {
			return 1
		}
		runner.Args = []string{"flake", "-local=true",
			"-pprof", ":6060",
			"-input-dir", *inputDir,
			"-output-dir", "/mnt/output",
			"-max-variants", fmt.Sprintf("%d", cmd.filter.MaxVariants),
			"-min-coverage", fmt.Sprintf("%f", cmd.filter.MinCoverage),
			"-max-tag", fmt.Sprintf("%d", cmd.filter.MaxTag),
		}
		var output string
		output, err = runner.Run()
		if err != nil {
			return 1
		}
		fmt.Fprintln(stdout, output)
		return 0
	}

	tilelib := &tileLibrary{
		retainNoCalls:       true,
		retainTileSequences: true,
		compactGenomes:      map[string][]tileVariantID{},
	}
	err = tilelib.LoadDir(context.Background(), *inputDir)
	if err != nil {
		return 1
	}

	log.Info("filtering")
	cmd.filter.Apply(tilelib)
	log.Info("tidying")
	tilelib.Tidy()
	err = tilelib.WriteDir(*outputDir)
	if err != nil {
		return 1
	}
	return 0
}