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v0.11.1 Latest Latest Go to latest Published: Oct 26, 2023 License: MIT Imports: 18 Imported by: 0

Details

Valid go.mod file
Redistributable license
Tagged version
Stable version
Learn more about best practices

Repository

github.com/labdao/plex

Links

Open Source Insights

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

Constants ¶

This section is empty.

Variables ¶

View Source

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 ¶ added in v0.9.0

func ContainsUserIdAnnotation(slice []string) bool

func ExtractUserIDFromIOJson ¶ added in v0.9.0

func ExtractUserIDFromIOJson(ioJsonPath string) (string, error)

func PrintIOGraphStatus ¶ added in v0.7.0

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 ¶ added in v0.10.4

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 ¶ added in v0.10.0

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

func ReadIOList ¶

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

func SubmitIoList ¶ added in v0.11.0

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 ¶ added in v0.8.1

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 ¶ added in v0.8.1

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"`
}

Source Files ¶

View all Source files

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