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workflow.go
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workflow.go
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package cwl
import (
"fmt"
"github.com/MG-RAST/AWE/lib/logger"
"github.com/davecgh/go-spew/spew"
"github.com/mitchellh/mapstructure"
//"os"
"reflect"
//"strings"
//"gopkg.in/mgo.v2/bson"
)
type Workflow struct {
CWL_object_Impl `yaml:",inline" bson:",inline" json:",inline" mapstructure:",squash"`
CWL_class_Impl `yaml:",inline" bson:",inline" json:",inline" mapstructure:",squash"` // provides Id and Class fields
CWL_id_Impl `yaml:",inline" bson:",inline" json:",inline" mapstructure:",squash"`
Inputs []InputParameter `yaml:"inputs,omitempty" bson:"inputs,omitempty" json:"inputs,omitempty" mapstructure:"inputs,omitempty"`
Outputs []WorkflowOutputParameter `yaml:"outputs,omitempty" bson:"outputs,omitempty" json:"outputs,omitempty" mapstructure:"outputs,omitempty"`
Steps []WorkflowStep `yaml:"steps,omitempty" bson:"steps,omitempty" json:"steps,omitempty" mapstructure:"steps,omitempty"`
Requirements *[]Requirement `yaml:"requirements,omitempty" bson:"requirements,omitempty" json:"requirements,omitempty" mapstructure:"requirements,omitempty"` //[]Requirement
Hints []interface{} `yaml:"hints,omitempty" bson:"hints,omitempty" json:"hints,omitempty" mapstructure:"hints,omitempty"` // []Requirement TODO Hints may contain non-requirement objects. Give warning in those cases.
Label string `yaml:"label,omitempty" bson:"label,omitempty" json:"label,omitempty" mapstructure:"label,omitempty"`
Doc string `yaml:"doc,omitempty" bson:"doc,omitempty" json:"doc,omitempty" mapstructure:"doc,omitempty"`
CwlVersion CWLVersion `yaml:"cwlVersion,omitempty" bson:"cwlVersion,omitempty" json:"cwlVersion,omitempty" mapstructure:"cwlVersion,omitempty"`
Metadata map[string]interface{} `yaml:"metadata,omitempty" bson:"metadata,omitempty" json:"metadata,omitempty" mapstructure:"metadata,omitempty"`
}
func (w *Workflow) GetClass() string { return string(CWL_Workflow) }
//func (w *Workflow) GetId() string { return w.Id }
//func (w *Workflow) SetId(id string) { w.Id = id }
//func (w *Workflow) Is_CWL_minimal() {}
//func (w *Workflow) Is_Any() {}
func (w *Workflow) Is_process() {}
func GetMapElement(m map[interface{}]interface{}, key string) (value interface{}, err error) {
for k, v := range m {
k_str, ok := k.(string)
if ok {
if k_str == key {
value = v
return
}
}
}
err = fmt.Errorf("Element \"%s\" not found in map", key)
return
}
func NewWorkflowEmpty() (w Workflow) {
w = Workflow{}
w.Class = string(CWL_Workflow)
return w
}
func NewWorkflow(original interface{}, cwl_version CWLVersion) (workflow_ptr *Workflow, schemata []CWLType_Type, err error) {
// convert input map into input array
original, err = MakeStringMap(original)
if err != nil {
err = fmt.Errorf("(NewWorkflow) MakeStringMap returned: %s", err.Error())
return
}
workflow := NewWorkflowEmpty()
workflow_ptr = &workflow
switch original.(type) {
case map[string]interface{}:
object := original.(map[string]interface{})
var CwlVersion CWLVersion
cwl_version_if, ok := object["cwlVersion"]
if ok {
//CwlVersion = cwl_version_if.(string)
var cwl_version_str string
cwl_version_str, ok = cwl_version_if.(string)
if !ok {
err = fmt.Errorf("(NewWorkflow) Could not read CWLVersion (%s)", reflect.TypeOf(cwl_version_if))
return
}
CwlVersion = CWLVersion(cwl_version_str)
} else {
CwlVersion = cwl_version
}
if CwlVersion == "" {
fmt.Println("workflow without version:")
//spew.Dump(object)
err = fmt.Errorf("(NewWorkflow) CwlVersion empty")
return
}
inputs, ok := object["inputs"]
if ok {
object["inputs"], err = NewInputParameterArray(inputs, schemata)
if err != nil {
err = fmt.Errorf("(NewWorkflow) NewInputParameterArray returned: %s", err.Error())
return
}
}
outputs, ok := object["outputs"]
if ok {
object["outputs"], err = NewWorkflowOutputParameterArray(outputs, schemata)
if err != nil {
err = fmt.Errorf("(NewWorkflow) NewWorkflowOutputParameterArray returned: %s", err.Error())
return
}
}
// convert steps to array if it is a map
steps, ok := object["steps"]
if ok {
logger.Debug(3, "(NewWorkflow) Parsing steps in Workflow")
var schemata_new []CWLType_Type
schemata_new, object["steps"], err = CreateWorkflowStepsArray(steps, CwlVersion)
if err != nil {
err = fmt.Errorf("(NewWorkflow) CreateWorkflowStepsArray returned: %s", err.Error())
return
}
for i, _ := range schemata_new {
schemata = append(schemata, schemata_new[i])
}
} else {
err = fmt.Errorf("(NewWorkflow) Workflow has no steps ")
//spew.Dump(object)
return
}
requirements, ok := object["requirements"]
if ok {
var schemata_new []CWLType_Type
//fmt.Println("---- Workflow (before CreateRequirementArray) ----")
//spew.Dump(object)
object["requirements"], schemata_new, err = CreateRequirementArray(requirements)
if err != nil {
fmt.Println("---- Workflow ----")
spew.Dump(object)
fmt.Println("---- requirements ----")
spew.Dump(requirements)
err = fmt.Errorf("(NewWorkflow) CreateRequirementArray returned: %s", err.Error())
return
}
for i, _ := range schemata_new {
schemata = append(schemata, schemata_new[i])
}
}
//fmt.Printf("......WORKFLOW raw")
//spew.Dump(object)
//fmt.Printf("-- Steps found ------------") // WorkflowStep
//for _, step := range elem["steps"].([]interface{}) {
// spew.Dump(step)
//}
err = mapstructure.Decode(object, &workflow)
if err != nil {
err = fmt.Errorf("(NewWorkflow) error parsing workflow class: %s", err.Error())
return
}
//fmt.Printf(".....WORKFLOW")
//spew.Dump(workflow)
return
default:
err = fmt.Errorf("(NewWorkflow) Input type %s can not be parsed", reflect.TypeOf(original))
}
return
}