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package main
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import (
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"encoding/json"
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"fmt"
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"io/ioutil"
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"log"
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"os"
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)
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// CWL is the toplevel object that has all the grpah
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type CWL struct {
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Graph []Graph `json:"$graph"`
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CwlVersion string `json:"cwlVersion"`
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}
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type Hints struct {
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Class string `json:"class"`
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LoadListing string `json:"loadListing"`
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}
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// Inputs are the pre-requisites for a step to run. Usually, files and directories
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// some of them coming from other steps
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type Inputs struct {
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ID string `json:"id"`
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Label string `json:"label"`
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//most types are just string, but sometimes you'll find things like:
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// "type": ["null", "Directory"]
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// "type": { "items": "string", "type": "array" }
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// or even:
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// "type": {
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// "items": { "items": ["File", "Directory"], "type": "array" },
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// "type": "array"
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// }
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Type interface{} `json:"type"`
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}
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/*
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// this is for outputs
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type Type struct {
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Items string `json:"items"`
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Type string `json:"type"`
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}*/
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// Outputs are the produced files, directories, etc. from Steps
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type Outputs struct {
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ID string `json:"id"`
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Label string `json:"label"`
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OutputSource string `json:"outputSource"`
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// most of the time this will be a {"items":...,"type":....}
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// but sometimes you'll find:
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// "type": "Directory"
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// or even:
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// "type": {
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// "items": { "items": "File", "type": "array" },
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// "type": "array"
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// }
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Type interface{} `json:"type"`
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}
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// Requirements is a list of requirements, usually a DockerPull will be signaling an image
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type Requirements struct {
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Class string `json:"class"`
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DockerPull string `json:"dockerPull,omitempty"`
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HTTPArvadosOrgCwlDockerCollectionPDH string `json:"http://arvados.org/cwl#dockerCollectionPDH,omitempty"`
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}
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type In struct {
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ID string `json:"id"`
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Source string `json:"source"`
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}
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// Steps is the central struct to define the acyclic graph of steps using In's and Out's
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type Steps struct {
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ID string `json:"id"`
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In []In `json:"in"`
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Out []string `json:"out"`
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Run string `json:"run"`
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// Scatter this could be a string for one step or an array for several steps
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Scatter interface{} `json:"scatter,omitempty"`
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}
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type Graph struct {
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Namespaces map[string]string `json:"$namespaces,omitempty"`
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Class string `json:"class"`
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Hints []Hints `json:"hints,omitempty"`
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ID string `json:"id"`
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Inputs []Inputs `json:"inputs"`
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Label string `json:"label,omitempty"`
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Outputs []Outputs `json:"outputs"`
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Requirements []Requirements `json:"requirements,omitempty"`
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Steps []Steps `json:"steps,omitempty"`
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// this is usually a []string with all the arguments,but
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// sometimes we can find things like:
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//"arguments": [
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// "$(inputs.bashscript)",
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// { "prefix": "-s", "valueFrom": "$(inputs.srclib)" },
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// { "prefix": "-n", "valueFrom": "$(inputs.newlib)" },
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// "bar",
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// "$(inputs.foo)"
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// ],
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Arguments []interface{} `json:"arguments,omitempty"`
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BaseCommand string `json:"baseCommand,omitempty"`
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Expression string `json:"expression,omitempty"`
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}
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//Dotty will give back a graph to print with dotty
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func Dotty(result CWL) string {
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const stepStyle = `[fillcolor="#FFD700", style="rounded,filled", shape=box]`
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const cmdStyle = `[fillcolor="#FF9912", style="rounded,filled", shape=box]`
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var nodes string
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var edges string
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for _, g := range result.Graph {
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if g.Class == "CommandLineTool" {
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nodes += fmt.Sprintf("\"cmd %s\" %s;\n", g.ID, cmdStyle)
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for _, input := range g.Inputs {
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edges += fmt.Sprintf("\"%s\" -> \"cmd %s\";\n", input.ID, g.ID)
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}
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for _, output := range g.Outputs {
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if output.OutputSource != "" {
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edges += fmt.Sprintf("\"cmd %s\" -> \"%s\";\n", g.ID, output.OutputSource)
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} else {
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edges += fmt.Sprintf("\"cmd %s\" -> \"%s\";\n", g.ID, output.ID)
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}
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}
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}
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for _, step := range g.Steps {
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nodes += fmt.Sprintf("\"step %s\" %s;\n", step.ID, stepStyle)
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for _, in := range step.In {
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if in.Source != "" {
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edges += fmt.Sprintf("\"%s\" -> \"step %s\";\n", in.Source, step.ID)
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} else {
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edges += fmt.Sprintf("\"%s\" -> \"step %s\";\n", in.ID, step.ID)
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}
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}
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// make all dependencies for outputs
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for _, out := range step.Out {
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edges += fmt.Sprintf("\"step %s\" -> \"%s\";\n", step.ID, out)
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}
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}
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}
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return fmt.Sprintf("digraph cwlgraph {\nrankdir=LR;\n\n%s\n\n%s}\n", nodes, edges)
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}
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func main() {
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// Open our jsonFile
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jsonFile, err := os.Open("su92l-xvhdp-3gri0mi1vtakaf4.json")
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// if we os.Open returns an error then handle it
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if err != nil {
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fmt.Println(err)
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}
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// defer the closing of our jsonFile so that we can parse it later on
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defer jsonFile.Close()
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byteValue, _ := ioutil.ReadAll(jsonFile)
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var result CWL
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err = json.Unmarshal([]byte(byteValue), &result)
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if err != nil {
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log.Fatalf("Error parsing json %v", err.Error())
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}
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fmt.Printf("%s\n", Dotty(result))
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}
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