Split database methods into RW and RO types and implement filestatus subcommand

cmd/filestatus.go

@@ -0,0 +1,261 @@
+package cmd
+
+import (
+	"crypto/md5" //nolint:gosec
+	"errors"
+	"fmt"
+	"io"
+	"os"
+	"path/filepath"
+	"sync"
+
+	"github.com/dustin/go-humanize" //nolint:misspell
+	"github.com/spf13/cobra"
+	"github.com/wtsi-hgi/ibackup/put"
+	"github.com/wtsi-hgi/ibackup/set"
+	"github.com/wtsi-npg/extendo/v2"
+)
+
+// options for this cmd.
+var filestatusIrods bool
+var filestatusDB string
+
+// statusCmd represents the status command.
+var filestatusCmd = &cobra.Command{
+	Use:   "filestatus",
+	Short: "Get the status of a file in the database",
+	Long: `Get the status of a file in the database.
+
+Prints out a summary of the given file for each set the file appears in.
+
+The --database option should be the path to the local backup of the iBackup
+database, defaulting to the value of the IBACKUP_LOCAL_DB_BACKUP_PATH
+environmental variable.
+
+The --irods options will gather additional information about the file, such as
+the local and remote checksums.
+`,
+	Run: func(cmd *cobra.Command, args []string) {
+		if len(args) < 1 {
+			die("you must supply the file to be checked")
+		}
+
+		err := fileSummary(filestatusDB, args[0], filestatusIrods)
+		if err != nil {
+			die(err.Error())
+		}
+	},
+}
+
+func init() {
+	RootCmd.AddCommand(filestatusCmd)
+
+	filestatusCmd.Flags().StringVarP(&filestatusDB, "database", "d",
+		os.Getenv("IBACKUP_LOCAL_DB_BACKUP_PATH"), "path to iBackup database file")
+	filestatusCmd.Flags().BoolVarP(&filestatusIrods, "irods", "i", false,
+		"do additional checking in iRods")
+}
+
+func fileSummary(dbPath, filePath string, useIrods bool) error {
+	db, err := set.NewRO(dbPath)
+	if err != nil {
+		return err
+	}
+
+	sets, err := db.GetAll()
+	if err != nil {
+		return err
+	}
+
+	fsg := newFSG(db, filePath, useIrods)
+
+	if fsg.baton != nil {
+		defer fsg.baton.StopIgnoreError()
+	}
+
+	if err := fsg.printFileStatuses(sets); err != nil {
+		return err
+	}
+
+	if !fsg.found {
+		cliPrint("file not found in any registered set\n")
+	}
+
+	return nil
+}
+
+type fileStatusGetter struct {
+	db       *set.DBRO
+	filePath string
+	baton    *extendo.Client
+	useIRods bool
+	found    bool
+
+	md5once sync.Once
+	md5sum  string
+}
+
+func newFSG(db *set.DBRO, filePath string, useIRods bool) *fileStatusGetter {
+	fsg := &fileStatusGetter{
+		db:       db,
+		filePath: filePath,
+		useIRods: useIRods,
+	}
+
+	if !useIRods {
+		return fsg
+	}
+
+	put.GetBatonHandler() //nolint:errcheck
+
+	if client, err := extendo.FindAndStart("--unbuffered", "--no-error"); err != nil {
+		warn("error occurred invoking baton; disabling irods mode: %s", err)
+
+		fsg.useIRods = false
+	} else {
+		fsg.baton = client
+	}
+
+	return fsg
+}
+
+func (fsg *fileStatusGetter) printFileStatuses(sets []*set.Set) error {
+	for _, set := range sets {
+		if err := fsg.printFileStatusIfInSet(set); err != nil {
+			return err
+		}
+	}
+
+	return nil
+}
+
+func (fsg *fileStatusGetter) printFileStatusIfInSet(s *set.Set) error {
+	entry, err := fsg.db.GetFileEntryForSet(s.ID(), fsg.filePath)
+	if err != nil {
+		var errr set.Error
+
+		if ok := errors.As(err, &errr); ok && errr.Msg == set.ErrInvalidEntry {
+			return nil
+		}
+
+		return err
+	}
+
+	if entry != nil {
+		fsg.found = true
+
+		if err := fsg.printFileStatus(s, entry); err != nil {
+			return err
+		}
+	}
+
+	return nil
+}
+
+func (fsg *fileStatusGetter) printFileStatus(set *set.Set, f *set.Entry) error {
+	dest, err := set.TransformPath(f.Path)
+	if err != nil {
+		return err
+	}
+
+	lastAttemptTime, err := put.TimeToMeta(f.LastAttempt)
+	if err != nil {
+		return err
+	}
+
+	cliPrint("file found in set: %s\n", set.Name)
+	cliPrint("           status: %s\n", f.Status)
+	cliPrint("             size: %s\n", humanize.IBytes(f.Size))
+	cliPrint("      destination: %s\n", dest)
+	cliPrint("   last attempted: %s\n", lastAttemptTime)
+
+	if f.LastError != "" {
+		cliPrint("       last error: %s\n", f.LastError)
+	}
+
+	if fsg.useIRods {
+		return fsg.printIRodsStatus(f.Path, dest)
+	}
+
+	return nil
+}
+
+func (fsg *fileStatusGetter) printIRodsStatus(local, remote string) error {
+	file, err := fsg.baton.ListItem(extendo.Args{AVU: true, Checksum: true}, extendo.RodsItem{
+		IPath: filepath.Dir(remote),
+		IName: filepath.Base(remote),
+	})
+	if err != nil {
+		return err
+	}
+
+	uploadDate, remoteMTime := fsg.getIrodsTimesFromAVUs(file.IAVUs)
+
+	if uploadDate != "" {
+		cliPrint("iRods upload date: %s\n", uploadDate)
+	}
+
+	if remoteMTime != "" {
+		localTime, err := getMTime(local)
+		if err != nil {
+			return err
+		}
+
+		cliPrint("      local mTime: %s\n", localTime)
+		cliPrint("      iRods mTime: %s\n", remoteMTime)
+	}
+
+	cliPrint("   iRods checksum: %s\n", file.IChecksum)
+	cliPrint("   local checksum: %s\n", fsg.calcMD5Sum(local))
+
+	return nil
+}
+
+func (fsg *fileStatusGetter) getIrodsTimesFromAVUs(avus []extendo.AVU) (string, string) {
+	var uploadDate, remoteMTime string
+
+	for _, avu := range avus {
+		if avu.Attr == put.MetaKeyDate {
+			uploadDate = avu.Value
+		}
+
+		if avu.Attr == put.MetaKeyMtime {
+			remoteMTime = avu.Value
+		}
+	}
+
+	return uploadDate, remoteMTime
+}
+
+func getMTime(local string) (string, error) {
+	stat, err := os.Stat(local)
+	if err != nil {
+		return "", err
+	}
+
+	return put.TimeToMeta(stat.ModTime())
+}
+
+func (fsg *fileStatusGetter) calcMD5Sum(path string) string {
+	fsg.md5once.Do(func() {
+		f, err := os.Open(path)
+		if err != nil {
+			fsg.md5sum = err.Error()
+
+			return
+		}
+
+		m := md5.New() //nolint:gosec
+
+		_, err = io.Copy(m, f)
+		f.Close()
+
+		if err != nil {
+			fsg.md5sum = err.Error()
+		} else {
+			fsg.md5sum = fmt.Sprintf("%x", m.Sum(nil))
+		}
+	})
+
+	return fsg.md5sum
+}

go.mod

@@ -101,7 +101,7 @@ require (
 	github.com/lestrrat-go/blackmagic v1.0.1 // indirect
 	github.com/lestrrat-go/httpcc v1.0.1 // indirect
 	github.com/lestrrat-go/iter v1.0.2 // indirect
-	github.com/lestrrat-go/jwx v1.2.25 // indirect
+	github.com/lestrrat-go/jwx v1.2.26 // indirect
 	github.com/lestrrat-go/option v1.0.1 // indirect
 	github.com/mattn/go-colorable v0.1.13 // indirect
 	github.com/mattn/go-isatty v0.0.19 // indirect

go.sum

@@ -43,6 +43,7 @@ github.com/davecgh/go-spew v1.1.0/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSs
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
 github.com/decred/dcrd/crypto/blake256 v1.0.0/go.mod h1:sQl2p6Y26YV+ZOcSTP6thNdn47hh8kt6rqSlvmrXFAc=
+github.com/decred/dcrd/crypto/blake256 v1.0.1/go.mod h1:2OfgNZ5wDpcsFmHmCK5gZTPcCXqlm2ArzUIkw9czNJo=
 github.com/decred/dcrd/dcrec/secp256k1/v4 v4.0.0-20210816181553-5444fa50b93d/go.mod h1:tmAIfUFEirG/Y8jhZ9M+h36obRZAk/1fcSpXwAVlfqE=
 github.com/decred/dcrd/dcrec/secp256k1/v4 v4.2.0 h1:8UrgZ3GkP4i/CLijOJx79Yu+etlyjdBU4sfcs2WYQMs=
 github.com/decred/dcrd/dcrec/secp256k1/v4 v4.2.0/go.mod h1:v57UDF4pDQJcEfFUCRop3lJL149eHGSe9Jvczhzjo/0=
@@ -239,8 +240,8 @@ github.com/lestrrat-go/iter v1.0.1/go.mod h1:zIdgO1mRKhn8l9vrZJZz9TUMMFbQbLeTsbq
 github.com/lestrrat-go/iter v1.0.2 h1:gMXo1q4c2pHmC3dn8LzRhJfP1ceCbgSiT9lUydIzltI=
 github.com/lestrrat-go/iter v1.0.2/go.mod h1:Momfcq3AnRlRjI5b5O8/G5/BvpzrhoFTZcn06fEOPt4=
 github.com/lestrrat-go/jwx v1.2.18/go.mod h1:bWTBO7IHHVMtNunM8so9MT8wD+euEY1PzGEyCnuI2qM=
-github.com/lestrrat-go/jwx v1.2.25 h1:tAx93jN2SdPvFn08fHNAhqFJazn5mBBOB8Zli0g0otA=
-github.com/lestrrat-go/jwx v1.2.25/go.mod h1:zoNuZymNl5lgdcu6P7K6ie2QRll5HVfF4xwxBBK1NxY=
+github.com/lestrrat-go/jwx v1.2.26 h1:4iFo8FPRZGDYe1t19mQP0zTRqA7n8HnJ5lkIiDvJcB0=
+github.com/lestrrat-go/jwx v1.2.26/go.mod h1:MaiCdGbn3/cckbOFSCluJlJMmp9dmZm5hDuIkx8ftpQ=
 github.com/lestrrat-go/option v0.0.0-20210103042652-6f1ecfceda35/go.mod h1:5ZHFbivi4xwXxhxY9XHDe2FHo6/Z7WWmtT7T5nBBp3I=
 github.com/lestrrat-go/option v1.0.0/go.mod h1:5ZHFbivi4xwXxhxY9XHDe2FHo6/Z7WWmtT7T5nBBp3I=
 github.com/lestrrat-go/option v1.0.1 h1:oAzP2fvZGQKWkvHa1/SAcFolBEca1oN+mQ7eooNBEYU=
@@ -367,8 +368,9 @@ github.com/stretchr/testify v1.7.2/go.mod h1:R6va5+xMeoiuVRoj+gSkQ7d3FALtqAAGI1F
 github.com/stretchr/testify v1.8.0/go.mod h1:yNjHg4UonilssWZ8iaSj1OCr/vHnekPRkoO+kdMU+MU=
 github.com/stretchr/testify v1.8.1/go.mod h1:w2LPCIKwWwSfY2zedu0+kehJoqGctiVI29o6fzry7u4=
 github.com/stretchr/testify v1.8.2/go.mod h1:w2LPCIKwWwSfY2zedu0+kehJoqGctiVI29o6fzry7u4=
-github.com/stretchr/testify v1.8.3 h1:RP3t2pwF7cMEbC1dqtB6poj3niw/9gnV4Cjg5oW5gtY=
 github.com/stretchr/testify v1.8.3/go.mod h1:sz/lmYIOXD/1dqDmKjjqLyZ2RngseejIcXlSw2iwfAo=
+github.com/stretchr/testify v1.8.4 h1:CcVxjf3Q8PM0mHUKJCdn+eZZtm5yQwehR5yeSVQQcUk=
+github.com/stretchr/testify v1.8.4/go.mod h1:sz/lmYIOXD/1dqDmKjjqLyZ2RngseejIcXlSw2iwfAo=
 github.com/thanhpk/randstr v1.0.6 h1:psAOktJFD4vV9NEVb3qkhRSMvYh4ORRaj1+w/hn4B+o=
 github.com/thanhpk/randstr v1.0.6/go.mod h1:M/H2P1eNLZzlDwAzpkkkUvoyNNMbzRGhESZuEQk3r0U=
 github.com/tidwall/gjson v1.14.3 h1:9jvXn7olKEHU1S9vwoMGliaT8jq1vJ7IH/n9zD9Dnlw=
@@ -425,7 +427,6 @@ golang.org/x/crypto v0.0.0-20201217014255-9d1352758620/go.mod h1:jdWPYTVW3xRLrWP
 golang.org/x/crypto v0.0.0-20210711020723-a769d52b0f97/go.mod h1:GvvjBRRGRdwPK5ydBHafDWAxML/pGHZbMvKqRZ5+Abc=
 golang.org/x/crypto v0.0.0-20210921155107-089bfa567519/go.mod h1:GvvjBRRGRdwPK5ydBHafDWAxML/pGHZbMvKqRZ5+Abc=
 golang.org/x/crypto v0.0.0-20211215153901-e495a2d5b3d3/go.mod h1:IxCIyHEi3zRg3s0A5j5BB6A9Jmi73HwBIUl50j+osU4=
-golang.org/x/crypto v0.0.0-20220427172511-eb4f295cb31f/go.mod h1:IxCIyHEi3zRg3s0A5j5BB6A9Jmi73HwBIUl50j+osU4=
 golang.org/x/crypto v0.0.0-20220622213112-05595931fe9d/go.mod h1:IxCIyHEi3zRg3s0A5j5BB6A9Jmi73HwBIUl50j+osU4=
 golang.org/x/crypto v0.0.0-20220829220503-c86fa9a7ed90/go.mod h1:IxCIyHEi3zRg3s0A5j5BB6A9Jmi73HwBIUl50j+osU4=
 golang.org/x/crypto v0.4.0/go.mod h1:3quD/ATkf6oY+rnes5c3ExXTbLc8mueNue5/DoinL80=
@@ -435,6 +436,7 @@ golang.org/x/mod v0.2.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
 golang.org/x/mod v0.3.0/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
 golang.org/x/mod v0.4.1/go.mod h1:s0Qsj1ACt9ePp/hMypM3fl4fZqREWJwdYDEqhRiZZUA=
 golang.org/x/mod v0.6.0-dev.0.20220419223038-86c51ed26bb4/go.mod h1:jJ57K6gSWd91VN4djpZkiMVwK6gcyfeH4XE8wZrZaV4=
+golang.org/x/mod v0.8.0/go.mod h1:iBbtSCu2XBx23ZKBPSOrRkjjQPZFPuis4dIYUhu/chs=
 golang.org/x/mod v0.10.0 h1:lFO9qtOdlre5W1jxS3r/4szv2/6iXxScdzjoBMXNhYk=
 golang.org/x/mod v0.10.0/go.mod h1:iBbtSCu2XBx23ZKBPSOrRkjjQPZFPuis4dIYUhu/chs=
 golang.org/x/net v0.0.0-20190311183353-d8887717615a/go.mod h1:t9HGtf8HONx5eT2rtn7q6eTqICYqUVnKs3thJo3Qplg=
@@ -452,6 +454,7 @@ golang.org/x/net v0.0.0-20211112202133-69e39bad7dc2/go.mod h1:9nx3DQGgdP8bBQD5qx
 golang.org/x/net v0.0.0-20220722155237-a158d28d115b/go.mod h1:XRhObCWvk6IyKnWLug+ECip1KBveYUHfp+8e9klMJ9c=
 golang.org/x/net v0.3.0/go.mod h1:MBQ8lrhLObU/6UmLb4fmbmk5OcyYmqtbGd/9yIeKjEE=
 golang.org/x/net v0.4.0/go.mod h1:MBQ8lrhLObU/6UmLb4fmbmk5OcyYmqtbGd/9yIeKjEE=
+golang.org/x/net v0.6.0/go.mod h1:2Tu9+aMcznHK/AK1HMvgo6xiTLG5rD5rZLDS+rp2Bjs=
 golang.org/x/net v0.10.0 h1:X2//UzNDwYmtCLn7To6G58Wr6f5ahEAQgKNzv9Y951M=
 golang.org/x/net v0.10.0/go.mod h1:0qNGK6F8kojg2nk9dLZ2mShWaEBan6FAoqfSigmmuDg=
 golang.org/x/oauth2 v0.8.0 h1:6dkIjl3j3LtZ/O3sTgZTMsLKSftL/B8Zgq4huOIIUu8=
@@ -462,6 +465,7 @@ golang.org/x/sync v0.0.0-20200625203802-6e8e738ad208/go.mod h1:RxMgew5VJxzue5/jJ
 golang.org/x/sync v0.0.0-20201020160332-67f06af15bc9/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
 golang.org/x/sync v0.0.0-20201207232520-09787c993a3a/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
 golang.org/x/sync v0.0.0-20220722155255-886fb9371eb4/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
+golang.org/x/sync v0.1.0/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
 golang.org/x/sync v0.2.0 h1:PUR+T4wwASmuSTYdKjYHI5TD22Wy5ogLU5qZCOLxBrI=
 golang.org/x/sync v0.2.0/go.mod h1:RxMgew5VJxzue5/jJTE5uejpjVlOe/izrB70Jof72aM=
 golang.org/x/sys v0.0.0-20180830151530-49385e6e1522/go.mod h1:STP8DvDyc/dI5b8T5hshtkjS+E42TnysNCUPdjciGhY=
@@ -492,13 +496,15 @@ golang.org/x/sys v0.0.0-20220811171246-fbc7d0a398ab/go.mod h1:oPkhp1MJrh7nUepCBc
 golang.org/x/sys v0.0.0-20220908164124-27713097b956/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
 golang.org/x/sys v0.2.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
 golang.org/x/sys v0.3.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
+golang.org/x/sys v0.5.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
 golang.org/x/sys v0.6.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
 golang.org/x/sys v0.8.0 h1:EBmGv8NaZBZTWvrbjNoL6HVt+IVy3QDQpJs7VRIw3tU=
 golang.org/x/sys v0.8.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
 golang.org/x/term v0.0.0-20201117132131-f5c789dd3221/go.mod h1:Nr5EML6q2oocZ2LXRh80K7BxOlk5/8JxuGnuhpl+muw=
 golang.org/x/term v0.0.0-20201126162022-7de9c90e9dd1/go.mod h1:bj7SfCRtBDWHUb9snDiAeCFNEtKQo2Wmx5Cou7ajbmo=
 golang.org/x/term v0.0.0-20210927222741-03fcf44c2211/go.mod h1:jbD1KX2456YbFQfuXm/mYQcufACuNUgVhRMnK/tPxf8=
 golang.org/x/term v0.3.0/go.mod h1:q750SLmJuPmVoN1blW3UFBPREJfb1KmY3vwxfr+nFDA=
+golang.org/x/term v0.5.0/go.mod h1:jMB1sMXY+tzblOD4FWmEbocvup2/aLOaQEp7JmGp78k=
 golang.org/x/term v0.8.0 h1:n5xxQn2i3PC0yLAbjTpNT85q/Kgzcr2gIoX9OrJUols=
 golang.org/x/term v0.8.0/go.mod h1:xPskH00ivmX89bAKVGSKKtLOWNx2+17Eiy94tnKShWo=
 golang.org/x/text v0.3.0/go.mod h1:NqM8EUOU14njkJ3fqMW+pc6Ldnwhi/IjpwHt7yyuwOQ=
@@ -508,6 +514,7 @@ golang.org/x/text v0.3.6/go.mod h1:5Zoc/QRtKVWzQhOtBMvqHzDpF6irO9z98xDceosuGiQ=
 golang.org/x/text v0.3.7/go.mod h1:u+2+/6zg+i71rQMx5EYifcz6MCKuco9NR6JIITiCfzQ=
 golang.org/x/text v0.4.0/go.mod h1:mrYo+phRRbMaCq/xk9113O4dZlRixOauAjOtrjsXDZ8=
 golang.org/x/text v0.5.0/go.mod h1:mrYo+phRRbMaCq/xk9113O4dZlRixOauAjOtrjsXDZ8=
+golang.org/x/text v0.7.0/go.mod h1:mrYo+phRRbMaCq/xk9113O4dZlRixOauAjOtrjsXDZ8=
 golang.org/x/text v0.9.0 h1:2sjJmO8cDvYveuX97RDLsxlyUxLl+GHoLxBiRdHllBE=
 golang.org/x/text v0.9.0/go.mod h1:e1OnstbJyHTd6l/uOt8jFFHp6TRDWZR/bV3emEE/zU8=
 golang.org/x/time v0.3.0 h1:rg5rLMjNzMS1RkNLzCG38eapWhnYLFYXDXj2gOlr8j4=
@@ -521,6 +528,7 @@ golang.org/x/tools v0.0.0-20210106214847-113979e3529a/go.mod h1:emZCQorbCU4vsT4f
 golang.org/x/tools v0.0.0-20210114065538-d78b04bdf963/go.mod h1:emZCQorbCU4vsT4fOWvOPXz4eW1wZW4PmDk9uLelYpA=
 golang.org/x/tools v0.1.0/go.mod h1:xkSsbof2nBLbhDlRMhhhyNLN/zl3eTqcnHD5viDpcZ0=
 golang.org/x/tools v0.1.12/go.mod h1:hNGJHUnrk76NpqgfD5Aqm5Crs+Hm0VOH/i9J2+nxYbc=
+golang.org/x/tools v0.6.0/go.mod h1:Xwgl3UAJ/d3gWutnCtw505GrjyAbvKui8lOU390QaIU=
 golang.org/x/tools v0.9.2 h1:UXbndbirwCAx6TULftIfie/ygDNCwxEie+IiNP1IcNc=
 golang.org/x/tools v0.9.2/go.mod h1:owI94Op576fPu3cIGQeHs3joujW/2Oc6MtlxbF5dfNc=
 golang.org/x/xerrors v0.0.0-20190717185122-a985d3407aa7/go.mod h1:I/5z698sn9Ka8TeJc9MKroUUfqBBauWjQqLJ2OPfmY0=