Merge branch 'version-0.2'

README.md

@@ -28,11 +28,14 @@ ChemCLI tool supports the following versions of Chemotion ELN:
 
 | ELN Version                                                            | `docker-compose.yml` file                                                                                                            | Supported by chemCLI version                                  |
 | ---------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------ | ------------------------------------------------------------- |
+| [v1.9.x](https://github.com/ComPlat/chemotion_ELN/releases/tag/v1.9.3) | [eln-1.9.3](https://raw.githubusercontent.com/Chemotion/ChemOrc/b7ad83fba1e1db6c5525a11b06bf7eed59a769f6/payload/docker-compose.yml) | [0.2.x](https://github.com/Chemotion/ChemCLI/releases/latest) |
 | [v1.8.x](https://github.com/ComPlat/chemotion_ELN/releases/tag/v1.8.2) | [eln-1.8.2](https://raw.githubusercontent.com/Chemotion/ChemCLI/7a62248a40416586e5d5e7d1a77adb6fe4f360fe/payload/docker-compose.yml) | [0.2.x](https://github.com/Chemotion/ChemCLI/releases/latest) |
 | [v1.7.x](https://github.com/ComPlat/chemotion_ELN/releases/tag/v1.7.3) | [eln-1.7.3](https://raw.githubusercontent.com/Chemotion/ChemCLI/b8bb1280a6e042b96b8d3e71d030709b113686bc/payload/docker-compose.yml) | [0.2.x](https://github.com/Chemotion/ChemCLI/releases/latest) |
 | [v1.6.x](https://github.com/ComPlat/chemotion_ELN/releases/tag/v1.6.2) | [eln-1.6.2](https://raw.githubusercontent.com/Chemotion/ChemCLI/e577832edaba14fa21ee9aa9288e4b00052729c8/payload/docker-compose.yml) | [0.2.x](https://github.com/Chemotion/ChemCLI/releases/latest) |
 
-> Chemotion ELN version [1.4.x](https://github.com/ComPlat/chemotion_ELN/releases/tag/v1.4.1-3) is **not supported** because it requires [manual changes](https://chemotion.net/docs/eln/install_configure/manual_install#only-when-installing-or-upgrading-to-version-141) to the installation after downloading the [`docker-compose.yml`](https://raw.githubusercontent.com/ptrxyz/chemotion/ba4b4620ab2aaa6be32df78189c29970335b1989/docker-compose.yml) file.
+> Chemotion ELN versions 1.9.0 and 1.9.1 were not released as dockerized images, and therefore cannot be installed using this tool.
+
+> Chemotion ELN versions 1.5.x and below are not supported. Kindly update your instance as soon as possible. If required, please contact the [helpdesk](https://chemotion.net/helpdesk).
 
 ## Concept for chemCLI
 

cli/prompt.go

@@ -130,8 +130,10 @@ func fileValidate(input string) (err error) {
 // kind of opposite of instanceValidate
 func newInstanceValidate(input string) (err error) {
 	err = textValidate(input)
-	if strings.ContainsRune(input, '.') {
-		err = toError("cannot have `.` in an instance name")
+	for _, char := range []rune{'.', '/', '\\', ':'} {
+		if strings.ContainsRune(input, char) {
+			err = toError("cannot have `%c` in an instance name", char)
+		}
 	}
 	if toLower(input) != input {
 		err = toError("cannot have an uppercase letter") // because case is not preserved by Viper v1.x

cli/root-instance-backup.go

@@ -3,29 +3,32 @@ package cli
 import (
 	"strings"
 
-	"github.com/chigopher/pathlib"
 	"github.com/spf13/cobra"
 )
 
 func instanceBackup(givenName, portion string) {
-	calledCmd := toSprintf("--profile execution run --rm -e BACKUP_WHAT=%s executor chemotion backup", portion)
-	var backupFile pathlib.Path
-	if strings.HasSuffix(conf.GetString(joinKey(instancesWord, currentInstance, "image")), "eln-1.3.1p220712") {
-		backupFile = downloadFile(backupshURL, "temp.backup.sh")
-		var err error
-		var output string
-		var out []byte
-		commands := []string{"create --name backcon ptrxyz/chemotion:eln-1.3.1p220712", "cp temp.backup.sh backcon:/embed/scripts/backup.sh", "commit backcon ptrxyz/chemotion:eln-1.3.1p220712", "rm backcon"}
-		for _, comm := range commands {
-			out, err = execShell(toSprintf("%s %s", virtualizer, comm))
-			output = toSprintf("%s %s", output, out)
-			if err != nil {
-				zboth.Fatal().Err(err).Msgf("command failed: %s %s", virtualizer, comm)
+	if strings.HasSuffix(conf.GetString(joinKey(instancesWord, givenName, "image")), "eln-1.3.1p220712") {
+		func() { // for version 1.3.1p220712
+
+			backupFile := downloadFile(backupshURL, "temp.backup.sh")
+			var (
+				err    error
+				output string
+				out    []byte
+			)
+			commands := []string{"create --name backcon ptrxyz/chemotion:eln-1.3.1p220712", "cp temp.backup.sh backcon:/embed/scripts/backup.sh", "commit backcon ptrxyz/chemotion:eln-1.3.1p220712", "rm backcon"}
+			for _, comm := range commands {
+				out, err = execShell(toSprintf("%s %s", virtualizer, comm))
+				output = toSprintf("%s %s", output, out)
+				if err != nil {
+					zboth.Fatal().Err(err).Msgf("command failed: %s %s", virtualizer, comm)
+				}
 			}
-		}
-		zboth.Debug().Msgf(output)
-		backupFile.Remove()
+			zboth.Debug().Msgf(output)
+			backupFile.Remove()
+		}()
 	}
+	calledCmd := toSprintf("--profile execution run --rm -e BACKUP_WHAT=%s executor chemotion backup", portion)
 	if _, successBackUp, _ := gotoFolder(givenName), callVirtualizer(composeCall+calledCmd), gotoFolder("work.dir"); successBackUp {
 		zboth.Info().Msgf("Backup successful.")
 	} else {

cli/root-instance-new.go

@@ -15,12 +15,12 @@ import (
 // helper to determine the required compose file
 func getComposeAddressToUse(currentVersion, action string) (use string) {
 	versions := make(map[string]string)
-	latestForThisCLIRelease := "1.8.2"
-	orderVersions := []string{latestForThisCLIRelease, "1.8.1", "1.7.3", "1.6.2"} // descending order
-	versions[latestForThisCLIRelease] = "https://raw.githubusercontent.com/Chemotion/ChemCLI/7a62248a40416586e5d5e7d1a77adb6fe4f360fe/payload/docker-compose.yml"
-	versions["1.8.1"] = "https://raw.githubusercontent.com/Chemotion/ChemCLI/681cab48409d6c9a6be51ac5903e04890467d998/payload/docker-compose.yml"
+	latestForThisCLIRelease := "1.9.3"
+	orderVersions := []string{latestForThisCLIRelease, "1.9.2", "1.8.2", "1.7.3"} // descending order
+	versions[latestForThisCLIRelease] = "https://raw.githubusercontent.com/Chemotion/ChemCLI/b7ad83fba1e1db6c5525a11b06bf7eed59a769f6/payload/docker-compose.yml"
+	versions["1.9.2"] = "https://raw.githubusercontent.com/Chemotion/ChemCLI/f30d8ae2dfdfb0160c3ceef30d5540e404c4f23a/payload/docker-compose.yml"
+	versions["1.8.2"] = "https://raw.githubusercontent.com/Chemotion/ChemCLI/7a62248a40416586e5d5e7d1a77adb6fe4f360fe/payload/docker-compose.yml"
 	versions["1.7.3"] = "https://raw.githubusercontent.com/Chemotion/ChemCLI/b8bb1280a6e042b96b8d3e71d030709b113686bc/payload/docker-compose.yml"
-	versions["1.6.2"] = "https://raw.githubusercontent.com/Chemotion/ChemCLI/e577832edaba14fa21ee9aa9288e4b00052729c8/payload/docker-compose.yml"
 	validVersions := []string{}
 	for _, version := range orderVersions {
 		now, _ := vercompare.NewVersion(currentVersion)
@@ -118,12 +118,6 @@ func getFreshPort(kind string) (port uint64) {
 	return
 }
 
-// to create a development instance
-func instanceCreateDevelopment(details map[string]string) (success bool) {
-	zboth.Fatal().Err(toError("not implemented")).Msgf("This feature - development instances of chemotion - is currently under development.")
-	return false
-}
-
 func createExtendedCompose(details map[string]string, use string) (extendedCompose viper.Viper) {
 	name := details["name"]
 	extendedCompose = *viper.New()
@@ -332,9 +326,7 @@ var newInstanceRootCmd = &cobra.Command{
 					zboth.Info().Msgf("Successfully created a new production instance. Once switched on, it can be found at: %s", details["accessAddress"])
 				}
 			case "Development":
-				if success := instanceCreateDevelopment(details); success {
-					zboth.Info().Msgf("Successfully created a new development instance.")
-				}
+				zboth.Fatal().Err(toError("not implemented")).Msgf("This feature - deployment of development instances of chemotion using ChemCLI - is currently under development.")
 			}
 		}
 	},

cli/root-instance-ping.go

@@ -8,7 +8,7 @@ import (
 )
 
 func instancePing(givenName string) (response string) {
-	url := conf.GetString(joinKey(instancesWord, currentInstance, "accessAddress"))
+	url := conf.GetString(joinKey(instancesWord, givenName, "accessAddress"))
 	client := http.Client{Timeout: 2 * time.Second}
 	if req, err := http.NewRequest("HEAD", url, nil); err == nil {
 		if resp, err := client.Do(req); err == nil {

cli/root.go

@@ -68,7 +68,7 @@ const (
 // configuration and logging
 var (
 	// version number, here to allow override
-	versionCLI = "0.2.16"
+	versionCLI = "0.2.17"
 	// current shell
 	shell string
 	// currently selected instance

go.mod

@@ -1,14 +1,14 @@
 module github.com/Chemotion/ChemCLI
 
-go 1.21
+go 1.22
 
 require (
 	github.com/cavaliergopher/grab/v3 v3.0.1
 	github.com/chigopher/pathlib v1.0.0
 	github.com/google/uuid v1.6.0
 	github.com/hashicorp/go-version v1.6.0
 	github.com/manifoldco/promptui v0.9.0
-	github.com/rs/zerolog v1.31.0
+	github.com/rs/zerolog v1.32.0
 	github.com/shirou/gopsutil v3.21.11+incompatible
 	github.com/spf13/cobra v1.8.0
 	github.com/spf13/viper v1.18.2
@@ -27,23 +27,23 @@ require (
 	github.com/mattn/go-isatty v0.0.20 // indirect
 	github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db
 	github.com/mitchellh/mapstructure v1.5.0 // indirect
-	github.com/pelletier/go-toml/v2 v2.1.1 // indirect
-	github.com/rivo/uniseg v0.4.4 // indirect
+	github.com/pelletier/go-toml/v2 v2.2.2 // indirect
+	github.com/rivo/uniseg v0.4.7 // indirect
 	github.com/rogpeppe/go-internal v1.12.0 // indirect
 	github.com/sagikazarmark/locafero v0.4.0 // indirect
 	github.com/sagikazarmark/slog-shim v0.1.0 // indirect
-	github.com/schollz/progressbar/v3 v3.14.1
+	github.com/schollz/progressbar/v3 v3.14.2
 	github.com/sourcegraph/conc v0.3.0 // indirect
 	github.com/spf13/afero v1.11.0 // indirect
 	github.com/spf13/cast v1.6.0 // indirect
 	github.com/spf13/pflag v1.0.5 // indirect
 	github.com/subosito/gotenv v1.6.0 // indirect
-	github.com/yusufpapurcu/wmi v1.2.3 // indirect
+	github.com/yusufpapurcu/wmi v1.2.4 // indirect
 	go.uber.org/multierr v1.11.0 // indirect
-	golang.org/x/exp v0.0.0-20240119083558-1b970713d09a // indirect
-	golang.org/x/sys v0.16.0 // indirect
-	golang.org/x/term v0.16.0 // indirect
-	golang.org/x/text v0.14.0 // indirect
+	golang.org/x/exp v0.0.0-20240506185415-9bf2ced13842 // indirect
+	golang.org/x/sys v0.20.0 // indirect
+	golang.org/x/term v0.20.0 // indirect
+	golang.org/x/text v0.15.0 // indirect
 	gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c // indirect
 	gopkg.in/ini.v1 v1.67.0 // indirect
 	gopkg.in/yaml.v3 v3.0.1 // indirect

go.sum

@@ -26,8 +26,8 @@ github.com/go-ole/go-ole v1.3.0 h1:Dt6ye7+vXGIKZ7Xtk4s6/xVdGDQynvom7xCFEdWr6uE=
 github.com/go-ole/go-ole v1.3.0/go.mod h1:5LS6F96DhAwUc7C+1HLexzMXY1xGRSryjyPPKW6zv78=
 github.com/godbus/dbus/v5 v5.0.4/go.mod h1:xhWf0FNVPg57R7Z0UbKHbJfkEywrmjJnf7w5xrFpKfA=
 github.com/google/go-cmp v0.5.2/go.mod h1:v8dTdLbMG2kIc/vJvl+f65V22dbkXbowE6jgT/gNBxE=
-github.com/google/go-cmp v0.5.9 h1:O2Tfq5qg4qc4AmwVlvv0oLiVAGB7enBSJ2x2DqQFi38=
-github.com/google/go-cmp v0.5.9/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY=
+github.com/google/go-cmp v0.6.0 h1:ofyhxvXcZhMsU5ulbFiLKl/XBFqE1GSq7atu8tAmTRI=
+github.com/google/go-cmp v0.6.0/go.mod h1:17dUlkBOakJ0+DkrSSNjCkIjxS6bF9zb3elmeNGIjoY=
 github.com/google/go-github v17.0.0+incompatible h1:N0LgJ1j65A7kfXrZnUDaYCs/Sf4rEjNlfyDHW9dolSY=
 github.com/google/go-github v17.0.0+incompatible/go.mod h1:zLgOLi98H3fifZn+44m+umXrS52loVEgC2AApnigrVQ=
 github.com/google/go-querystring v1.1.0 h1:AnCroh3fv4ZBgVIf1Iwtovgjaw/GiKJo8M8yD/fhyJ8=
@@ -62,26 +62,26 @@ github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db h1:62I3jR2Em
 github.com/mitchellh/colorstring v0.0.0-20190213212951-d06e56a500db/go.mod h1:l0dey0ia/Uv7NcFFVbCLtqEBQbrT4OCwCSKTEv6enCw=
 github.com/mitchellh/mapstructure v1.5.0 h1:jeMsZIYE/09sWLaz43PL7Gy6RuMjD2eJVyuac5Z2hdY=
 github.com/mitchellh/mapstructure v1.5.0/go.mod h1:bFUtVrKA4DC2yAKiSyO/QUcy7e+RRV2QTWOzhPopBRo=
-github.com/pelletier/go-toml/v2 v2.1.1 h1:LWAJwfNvjQZCFIDKWYQaM62NcYeYViCmWIwmOStowAI=
-github.com/pelletier/go-toml/v2 v2.1.1/go.mod h1:tJU2Z3ZkXwnxa4DPO899bsyIoywizdUvyaeZurnPPDc=
+github.com/pelletier/go-toml/v2 v2.2.2 h1:aYUidT7k73Pcl9nb2gScu7NSrKCSHIDE89b3+6Wq+LM=
+github.com/pelletier/go-toml/v2 v2.2.2/go.mod h1:1t835xjRzz80PqgE6HHgN2JOsmgYu/h4qDAS4n929Rs=
 github.com/pkg/errors v0.9.1/go.mod h1:bwawxfHBFNV+L2hUp1rHADufV3IMtnDRdf1r5NINEl0=
 github.com/pmezard/go-difflib v1.0.0/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
 github.com/pmezard/go-difflib v1.0.1-0.20181226105442-5d4384ee4fb2 h1:Jamvg5psRIccs7FGNTlIRMkT8wgtp5eCXdBlqhYGL6U=
 github.com/pmezard/go-difflib v1.0.1-0.20181226105442-5d4384ee4fb2/go.mod h1:iKH77koFhYxTK1pcRnkKkqfTogsbg7gZNVY4sRDYZ/4=
-github.com/rivo/uniseg v0.4.4 h1:8TfxU8dW6PdqD27gjM8MVNuicgxIjxpm4K7x4jp8sis=
-github.com/rivo/uniseg v0.4.4/go.mod h1:FN3SvrM+Zdj16jyLfmOkMNblXMcoc8DfTHruCPUcx88=
+github.com/rivo/uniseg v0.4.7 h1:WUdvkW8uEhrYfLC4ZzdpI2ztxP1I582+49Oc5Mq64VQ=
+github.com/rivo/uniseg v0.4.7/go.mod h1:FN3SvrM+Zdj16jyLfmOkMNblXMcoc8DfTHruCPUcx88=
 github.com/rogpeppe/go-internal v1.12.0 h1:exVL4IDcn6na9z1rAb56Vxr+CgyK3nn3O+epU5NdKM8=
 github.com/rogpeppe/go-internal v1.12.0/go.mod h1:E+RYuTGaKKdloAfM02xzb0FW3Paa99yedzYV+kq4uf4=
 github.com/rs/xid v1.5.0/go.mod h1:trrq9SKmegXys3aeAKXMUTdJsYXVwGY3RLcfgqegfbg=
-github.com/rs/zerolog v1.31.0 h1:FcTR3NnLWW+NnTwwhFWiJSZr4ECLpqCm6QsEnyvbV4A=
-github.com/rs/zerolog v1.31.0/go.mod h1:/7mN4D5sKwJLZQ2b/znpjC3/GQWY/xaDXUM0kKWRHss=
+github.com/rs/zerolog v1.32.0 h1:keLypqrlIjaFsbmJOBdB/qvyF8KEtCWHwobLp5l/mQ0=
+github.com/rs/zerolog v1.32.0/go.mod h1:/7mN4D5sKwJLZQ2b/znpjC3/GQWY/xaDXUM0kKWRHss=
 github.com/russross/blackfriday/v2 v2.1.0/go.mod h1:+Rmxgy9KzJVeS9/2gXHxylqXiyQDYRxCVz55jmeOWTM=
 github.com/sagikazarmark/locafero v0.4.0 h1:HApY1R9zGo4DBgr7dqsTH/JJxLTTsOt7u6keLGt6kNQ=
 github.com/sagikazarmark/locafero v0.4.0/go.mod h1:Pe1W6UlPYUk/+wc/6KFhbORCfqzgYEpgQ3O5fPuL3H4=
 github.com/sagikazarmark/slog-shim v0.1.0 h1:diDBnUNK9N/354PgrxMywXnAwEr1QZcOr6gto+ugjYE=
 github.com/sagikazarmark/slog-shim v0.1.0/go.mod h1:SrcSrq8aKtyuqEI1uvTDTK1arOWRIczQRv+GVI1AkeQ=
-github.com/schollz/progressbar/v3 v3.14.1 h1:VD+MJPCr4s3wdhTc7OEJ/Z3dAeBzJ7yKH/P4lC5yRTI=
-github.com/schollz/progressbar/v3 v3.14.1/go.mod h1:Zc9xXneTzWXF81TGoqL71u0sBPjULtEHYtj/WVgVy8E=
+github.com/schollz/progressbar/v3 v3.14.2 h1:EducH6uNLIWsr560zSV1KrTeUb/wZGAHqyMFIEa99ks=
+github.com/schollz/progressbar/v3 v3.14.2/go.mod h1:aQAZQnhF4JGFtRJiw/eobaXpsqpVQAftEQ+hLGXaRc4=
 github.com/shirou/gopsutil v3.21.11+incompatible h1:+1+c1VGhc88SSonWP6foOcLhvnKlUeu/erjjvaPEYiI=
 github.com/shirou/gopsutil v3.21.11+incompatible/go.mod h1:5b4v6he4MtMOwMlS0TUMTu2PcXUg8+E1lC7eC3UO/RA=
 github.com/sourcegraph/conc v0.3.0 h1:OQTbbt6P72L20UqAkXXuLOj79LfEanQ+YQFNpLA9ySo=
@@ -98,36 +98,38 @@ github.com/spf13/viper v1.18.2 h1:LUXCnvUvSM6FXAsj6nnfc8Q2tp1dIgUfY9Kc8GsSOiQ=
 github.com/spf13/viper v1.18.2/go.mod h1:EKmWIqdnk5lOcmR72yw6hS+8OPYcwD0jteitLMVB+yk=
 github.com/stretchr/objx v0.1.0/go.mod h1:HFkY916IF+rwdDfMAkV7OtwuqBVzrE8GR6GFx+wExME=
 github.com/stretchr/objx v0.4.0/go.mod h1:YvHI0jy2hoMjB+UWwv71VJQ9isScKT/TqJzVSSt89Yw=
-github.com/stretchr/objx v0.5.0 h1:1zr/of2m5FGMsad5YfcqgdqdWrIhu+EBEJRhR1U7z/c=
 github.com/stretchr/objx v0.5.0/go.mod h1:Yh+to48EsGEfYuaHDzXPcE3xhTkx73EhmCGUpEOglKo=
+github.com/stretchr/objx v0.5.2 h1:xuMeJ0Sdp5ZMRXx/aWO6RZxdr3beISkG5/G/aIRr3pY=
+github.com/stretchr/objx v0.5.2/go.mod h1:FRsXN1f5AsAjCGJKqEizvkpNtU+EGNCLh3NxZ/8L+MA=
 github.com/stretchr/testify v1.3.0/go.mod h1:M5WIy9Dh21IEIfnGCwXGc5bZfKNJtfHm1UVUgZn+9EI=
 github.com/stretchr/testify v1.7.1/go.mod h1:6Fq8oRcR53rry900zMqJjRRixrwX3KX962/h/Wwjteg=
 github.com/stretchr/testify v1.8.0/go.mod h1:yNjHg4UonilssWZ8iaSj1OCr/vHnekPRkoO+kdMU+MU=
-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/stretchr/testify v1.9.0 h1:HtqpIVDClZ4nwg75+f6Lvsy/wHu+3BoSGCbBAcpTsTg=
+github.com/stretchr/testify v1.9.0/go.mod h1:r2ic/lqez/lEtzL7wO/rwa5dbSLXVDPFyf8C91i36aY=
 github.com/subosito/gotenv v1.6.0 h1:9NlTDc1FTs4qu0DDq7AEtTPNw6SVm7uBMsUCUjABIf8=
 github.com/subosito/gotenv v1.6.0/go.mod h1:Dk4QP5c2W3ibzajGcXpNraDfq2IrhjMIvMSWPKKo0FU=
-github.com/yusufpapurcu/wmi v1.2.3 h1:E1ctvB7uKFMOJw3fdOW32DwGE9I7t++CRUEMKvFoFiw=
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