/
convert_bundle_parameters.go
228 lines (189 loc) · 6.89 KB
/
convert_bundle_parameters.go
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package cmd
import (
"encoding/json"
"fmt"
"os"
"strings"
"github.com/antha-lang/antha/antha/AnthaStandardLibrary/Packages/search"
"github.com/antha-lang/antha/antha/anthalib/wtype"
"github.com/antha-lang/antha/execute/executeutil"
"github.com/antha-lang/antha/workflow"
"github.com/spf13/cobra"
"github.com/spf13/viper"
)
var convertBundleCmd = &cobra.Command{
Use: "bundle-parameters",
Short: "update bundle parameters according to the map of old parameter names to new",
RunE: convertBundle,
}
type NewElementMappingDetails struct {
ConversionDetails `json:"new-element-mapping-details"`
}
type ConversionDetails struct {
OldElementName string `json:"old-element-name"`
NewElementName string `json:"new-element-name"`
NewParameterMapping map[string]string `json:"new-parameter-mapping"`
DeprecatedParameters []string `json:"deprecated-parameters"`
NewParameters map[string]json.RawMessage `json:"new-parameters"`
ParameterTypeChanges map[string]json.RawMessage `json:"parameter-type-changes"`
}
func (c NewElementMappingDetails) Empty() bool {
if c.ConversionDetails.OldElementName != "" || c.ConversionDetails.NewElementName != "" || len(c.ConversionDetails.NewParameterMapping) > 0 {
return false
}
return true
}
// replaces old parameter names with new; this must be done after changing parameter names
func convertProcesses(in map[string]workflow.Process, newElementNames ConversionDetails) map[string]workflow.Process {
ret := make(map[string]workflow.Process)
for k, v := range in {
var comp string
if v.Component == newElementNames.OldElementName {
comp = newElementNames.NewElementName
} else {
comp = v.Component
}
ret[k] = workflow.Process{
Component: comp,
Metadata: v.Metadata,
}
}
return ret
}
func containsSomethingToConvert(in executeutil.Bundle, newElementNames ConversionDetails) bool {
for _, element := range in.Processes {
if element.Component == newElementNames.OldElementName {
return true
}
}
return false
}
func convertParametersAndConnections(in executeutil.Bundle, newElementNames ConversionDetails) (map[string]map[string]json.RawMessage, []workflow.Connection, error) {
var errs []string
parameters := make(map[string]map[string]json.RawMessage)
connections := in.Connections
for processName, element := range in.Processes {
// check if element name is to be replaced or is already equal to new element name
// in order to suupport updating of parameter names.
if element.Component == newElementNames.OldElementName || element.Component == newElementNames.NewElementName {
// get existing parameters
parametersForThisProcess, found := in.Parameters[processName]
if !found {
panic(fmt.Errorf("parameters not found for %s", processName))
}
newParameters := make(map[string]json.RawMessage)
// update values of parameters according to map
for parameterName, value := range parametersForThisProcess {
// check for replacement parameter names
if newParameterName, newParameterFound := newElementNames.NewParameterMapping[parameterName]; newParameterFound {
newParameters[newParameterName] = value
} else if typeChangeDetails, typeChangeFound := newElementNames.ParameterTypeChanges[parameterName]; typeChangeFound {
errs = append(errs, fmt.Sprintf("detected a parameter %q of process %q requires type change of %s. Please manually convert this parameter", parameterName, processName, string(typeChangeDetails)))
} else if !search.InStrings(newElementNames.DeprecatedParameters, parameterName) {
newParameters[parameterName] = value
}
}
// add new defaults if any specified
for newParameterName, defaultValue := range newElementNames.NewParameters {
newParameters[newParameterName] = defaultValue
}
// replace connections
for parameterName, newParameterName := range newElementNames.NewParameterMapping {
for i := range connections {
connections[i] = replaceConnection(connections[i], processName, parameterName, newParameterName)
}
}
parameters[processName] = newParameters
} else {
parameters[processName] = in.Parameters[processName]
}
}
if len(errs) > 0 {
return parameters, connections, wtype.NewWarningf(strings.Join(errs, ";"))
}
return parameters, connections, nil
}
func replaceConnection(connection workflow.Connection, processToReplace, parameterToReplace, newParameterName string) workflow.Connection {
var newConnection workflow.Connection
if connection.Src.Process == processToReplace && connection.Src.Port == parameterToReplace {
newConnection.Src = workflow.Port{
Process: connection.Src.Process,
Port: newParameterName,
}
} else {
newConnection.Src = connection.Src
}
if connection.Tgt.Process == processToReplace && connection.Tgt.Port == parameterToReplace {
newConnection.Tgt = workflow.Port{
Process: connection.Tgt.Process,
Port: newParameterName,
}
} else {
newConnection.Tgt = connection.Tgt
}
return newConnection
}
type nothingToConvert struct {
ErrMessage string
}
func (err nothingToConvert) Error() string {
return err.ErrMessage
}
func convertBundleWithArgs(conversionMapFileName, bundleFileName, outPutFileName string) error {
cFile, err := os.Open(conversionMapFileName)
if err != nil {
return err
}
defer cFile.Close() // nolint
var c NewElementMappingDetails
decConv := json.NewDecoder(cFile)
if err := decConv.Decode(&c); err != nil {
return err
}
if c.Empty() {
return nothingToConvert{ErrMessage: "empty conversion map"}
}
inFile, err := os.Open(bundleFileName)
if err != nil {
return err
}
defer inFile.Close() // nolint
var original executeutil.Bundle
dec := json.NewDecoder(inFile)
if err := dec.Decode(&original); err != nil {
return err
}
var bundle executeutil.Bundle = original
if !containsSomethingToConvert(original, c.ConversionDetails) {
return nothingToConvert{ErrMessage: "nothing to convert in bundle file"}
}
var warning error
bundle.Parameters, bundle.Connections, warning = convertParametersAndConnections(original, c.ConversionDetails)
bundle.Processes = convertProcesses(original.Processes, c.ConversionDetails)
outFile, err := os.Create(outPutFileName)
if err != nil {
return err
}
defer outFile.Close() // nolint
enc := json.NewEncoder(outFile)
enc.SetIndent("", " ")
err = enc.Encode(bundle)
if err != nil {
return err
}
return warning
}
func convertBundle(cmd *cobra.Command, args []string) error {
if err := viper.BindPFlags(cmd.Flags()); err != nil {
return err
}
return convertBundleWithArgs(viper.GetString("conversionMap"), viper.GetString("bundle"), viper.GetString("output"))
}
func init() {
c := convertBundleCmd
convertCmd.AddCommand(c)
flags := c.Flags()
flags.String("bundle", "", "Input bundle")
flags.String("conversionMap", "", "conversion map file")
flags.String("output", "output.json", "default output bundle name in antha format")
}