ipwl

Documentation

Index

• Variables
• func ContainsUserIdAnnotation(slice []string) bool
• func ExtractUserIDFromIOJson(ioJsonPath string) (string, error)
• func PrintIOGraphStatus(ioList []IO)
• func ProcessIOList(jobDir, ioJsonPath, selector string, retry, verbose, showAnimation bool, ...)
• func ReadToolConfig(toolPath string) (Tool, ToolInfo, error)
• func RunIO(ioJsonCid, outputDir, selector string, verbose, showAnimation bool, ...) (completedIoJsonCid, ioJsonPath string, err error)
• func WriteIOList(ioJsonPath string, ioList []IO) error
• type ArrayFileOutput
  • func (afo ArrayFileOutput) OutputType() string
• type FileInput
• type FileOutput
  • func (fo FileOutput) OutputType() string
• type IO
  • func InitializeIo(toolPath string, scatteringMethod string, inputVectors map[string][]string) ([]IO, error)
  • func ReadIOList(filePath string) ([]IO, error)
  • func SubmitIoList(ioList []IO, selector string, maxTime int, annotations []string) []IO
  • func (io IO) MarshalJSON() ([]byte, error)
  • func (io *IO) UnmarshalJSON(data []byte) error
• type Output
• type OutputValues
• type Tool
• type ToolInfo
• type ToolInput
• type ToolOutput

Variables

var CORE_TOOLS = map[string]string{
	"equibind":             "QmZ2HarAgwZGjc3LBx9mWNwAQkPWiHMignqKup1ckp8NhB",
	"diffdock":             "QmSzetFkveiQYZ5FgpZdHHfsjMWYz5YzwMAvqUgUFhFPMM",
	"colabfold-mini":       "QmcRH74qfqDBJFku3mEDGxkAf6CSpaHTpdbe1pMkHnbcZD",
	"colabfold-standard":   "QmXnM1VpdGgX5huyU3zTjJovsu42KPfWhjxhZGkyvy9PVk",
	"colabfold-large":      "QmPYqMy19VFFuYztL6b5ruo4Kw4JWT583emStGrSYTH5Yi",
	"bam2fastq":            "QmbPUirWiWCv9sgdHLekf5AnoCdw4QPU2SyfGGKs9JRRbq",
	"oddt":                 "QmUx7NdxkXXZvbK1JXZVUYUBqsevWkbVxgTzpWJ4Xp4inf",
	"rfdiffusion":          "QmXnCBCtoYuPyGsEJVpjn5regHfFSYa8kx44e22XxDX2t2",
	"repeatmodeler":        "QmZdXxnUt1sFFR39CfkEUgiioUBf6qP5CUs8TCb7Wqn4MC",
	"gnina":                "QmYfGaWzxwi8HiWLdiX4iQXuuLXVKYrr6YC3DknEvZeSne",
	"batch-dlkcat":         "QmThdvypN8gDDwwyNnpSYsdwvyxCET8s1jym3HZCTaBzmD",
	"openbabel-pdb-to-sdf": "QmbbDSDZJp8G7EFaNKsT7Qe7S9iaaemZmyvS6XgZpdR5e3",
	"openbabel-rmsd":       "QmUxrKgAs5r42xVki4vtMskJa1Z7WA64wURkwywPMch7dA",
}

You can use custom tools by passing the cid directly to plex -t arguments

Functions

func ContainsUserIdAnnotation

func ContainsUserIdAnnotation(slice []string) bool

func ExtractUserIDFromIOJson

func ExtractUserIDFromIOJson(ioJsonPath string) (string, error)

func PrintIOGraphStatus

func PrintIOGraphStatus(ioList []IO)

func ProcessIOList

func ProcessIOList(jobDir, ioJsonPath, selector string, retry, verbose, showAnimation bool, maxTime int, annotations []string)

func ReadToolConfig

func ReadToolConfig(toolPath string) (Tool, ToolInfo, error)

func RunIO

func RunIO(ioJsonCid, outputDir, selector string, verbose, showAnimation bool, maxTime int, annotations []string) (completedIoJsonCid, ioJsonPath string, err error)

func WriteIOList

func WriteIOList(ioJsonPath string, ioList []IO) error

Types

type ArrayFileOutput

type ArrayFileOutput struct {
	Class string       `json:"class"`
	Files []FileOutput `json:"files"`
}

func (ArrayFileOutput) OutputType

func (afo ArrayFileOutput) OutputType() string

type FileInput

type FileInput struct {
	Class    string `json:"class"`
	FilePath string `json:"filepath"`
	IPFS     string `json:"ipfs"`
}

type FileOutput

type FileOutput struct {
	Class    string `json:"class"`
	FilePath string `json:"filepath"`
	IPFS     string `json:"ipfs"`
}

func (FileOutput) OutputType

func (fo FileOutput) OutputType() string

type IO

type IO struct {
	Tool          ToolInfo             `json:"tool"`
	Inputs        map[string]FileInput `json:"inputs"`
	Outputs       map[string]Output    `json:"outputs"`
	State         string               `json:"state"`
	ErrMsg        string               `json:"errMsg"`
	UserID        string               `json:"userId"`
	BacalhauJobId string               `json:"bacalhauJobId"`
}

func InitializeIo

func InitializeIo(toolPath string, scatteringMethod string, inputVectors map[string][]string) ([]IO, error)

func ReadIOList

func ReadIOList(filePath string) ([]IO, error)

func SubmitIoList

func SubmitIoList(ioList []IO, selector string, maxTime int, annotations []string) []IO

func (IO) MarshalJSON

func (io IO) MarshalJSON() ([]byte, error)

func (*IO) UnmarshalJSON

func (io *IO) UnmarshalJSON(data []byte) error

type Output

type Output interface {
	OutputType() string
}

type OutputValues

type OutputValues struct {
	FilePaths []string `json:"filePaths"`
	CIDs      []string `json:"cids"`
	CidPaths  []string `json:"cidPaths"`
}

type Tool

type Tool struct {
	Name        string                `json:"name"`
	Description string                `json:"description"`
	Author      string                `json:"author"`
	BaseCommand []string              `json:"baseCommand"`
	Arguments   []string              `json:"arguments"`
	DockerPull  string                `json:"dockerPull"`
	GpuBool     bool                  `json:"gpuBool"`
	MemoryGB    *int                  `json:"memoryGB"`
	NetworkBool bool                  `json:"networkBool"`
	Inputs      map[string]ToolInput  `json:"inputs"`
	Outputs     map[string]ToolOutput `json:"outputs"`
}

type ToolInfo

type ToolInfo struct {
	Name string `json:"name"`
	IPFS string `json:"ipfs"`
}

type ToolInput

type ToolInput struct {
	Type    string   `json:"type"`
	Glob    []string `json:"glob"`
	Default string   `json:"default"`
}

type ToolOutput

type ToolOutput struct {
	Type string   `json:"type"`
	Item string   `json:"item"`
	Glob []string `json:"glob"`
}