Documentation
¶
Overview ¶
Package nextflow contains reusable logic for working with Nextflow-based services:
- parsing ivcap.yaml / ivcap-tool.yaml from a pipeline archive
- generating the service description payload
- upload resume metadata helpers
- tar archive inspection helpers
It intentionally contains no Cobra / CLI printing. (Note: it may still write small progress/status messages via the provided zap.Logger, consistent with other pkg/* helpers.)
Index ¶
- Constants
- func DrainTar(r io.Reader) ([]string, error)
- func ExtractFileFromTarBytes(archive []byte, fileName string) ([]byte, string, error)
- func ExtractFileFromTarPath(archivePath string, fileName string) (content []byte, foundPath string, err error)
- func ExtractFileFromTarReader(tr *tar.Reader, targetName string) (content []byte, foundPath string, err error)
- func ExtractFromTarAuto(data []byte, innerPath string) ([]byte, string, error)
- func GuessArchiveContentType(p string) string
- func ReadUploadMeta(archivePath string, size int64, mtimeUnix int64) (artifactID string, ok bool)
- func SanitizeTarPath(p string) (string, error)
- func TarGzFromSources(ctx context.Context, sources []Source, adpt *a.Adapter, logger *log.Logger, ...) ([]byte, string, error)
- func UploadArchiveAsArtifact(ctxt context.Context, toolName string, archivePath string, chunkSize int64, ...) (artifactID string, err error)
- func UploadMetaPath(archivePath string) string
- func UpsertServiceDescriptionAspect(ctxt context.Context, entityServiceID string, svc *ServiceDescription, ...) (aspectID string, err error)
- func ValidateFnSchema(m map[string]any) error
- func WriteUploadMeta(archivePath string, size int64, mtimeUnix int64, artifactID string)
- type CreateOutput
- type ServiceDescription
- type SimpleProperty
- type SimpleToolHeader
- type Source
- type ToolHeader
- type UploadMeta
Constants ¶
const ( ServiceSchema = "urn:ivcap:schema.service.2" ServiceControllerURN = "urn:ivcap:schema.service.nextflow.1" ServiceDefaultPolicy = "urn:ivcap:policy:ivcap.open.service" ServiceMainScriptName = "main.nf" )
const SimpleToolFileName = "ivcap.yaml"
Optional, simplified manifest. If present in the archive, this file is preferred over ivcap-tool.yaml and will be converted to the richer ivcap-tool structure internally.
const ToolFileName = "ivcap-tool.yaml"
const UploadMetaPrefix = ".ivcap-nextflow-"
Variables ¶
This section is empty.
Functions ¶
func ExtractFileFromTarBytes ¶
ExtractFileFromTarBytes extracts a file from a tar or tar.gz archive represented as bytes.
func ExtractFileFromTarPath ¶
func ExtractFromTarAuto ¶
ExtractFromTarAuto extracts a file from tar or tar.gz bytes.
func GuessArchiveContentType ¶
func ReadUploadMeta ¶
func SanitizeTarPath ¶
SanitizeTarPath validates and normalizes a file path intended to be stored inside a tar archive.
It ensures a stable unix-style relative path, disallows traversal and volume names, and rejects empty/invalid names.
func TarGzFromSources ¶
func TarGzFromSources( ctx context.Context, sources []Source, adpt *a.Adapter, logger *log.Logger, fetchURLBytes func(context.Context, string) ([]byte, string, error), downloadArtifactBytes func(context.Context, string, *a.Adapter) ([]byte, error), ) ([]byte, string, error)
TarGzFromSources assembles a tar.gz from the provided sources and also returns a compact JSON manifest string (suitable for storing in artifact meta).
`fetchURLBytes` and `downloadArtifactBytes` are injected to keep this package independent of cmd/* MCP helpers.
func UploadArchiveAsArtifact ¶
func UploadArchiveAsArtifact( ctxt context.Context, toolName string, archivePath string, chunkSize int64, adapter *a.Adapter, silent bool, logger *log.Logger, ) (artifactID string, err error)
UploadArchiveAsArtifact uploads a local archive file as an IVCAP artifact and supports resuming interrupted uploads via local UploadMeta.
Notes:
- archivePath must be a local path ("-" is not supported)
- chunkSize should typically be cmd.DEF_CHUNK_SIZE
func UploadMetaPath ¶
func UpsertServiceDescriptionAspect ¶
func UpsertServiceDescriptionAspect(ctxt context.Context, entityServiceID string, svc *ServiceDescription, adapter *a.Adapter, logger *log.Logger) (aspectID string, err error)
UpsertServiceDescriptionAspect publishes a service description as a Data Fabric aspect.
Entity: service ID Schema: svc.Schema
func ValidateFnSchema ¶
Types ¶
type CreateOutput ¶
type CreateOutput struct {
OK bool `yaml:"ok" json:"ok"`
ServiceID string `yaml:"service-id" json:"service-id"`
PipelineArtifactURN string `yaml:"pipeline" json:"pipeline"`
ServiceAspectRecordID string `yaml:"service-aspect" json:"service-aspect"`
ServiceDescription *ServiceDescription `yaml:"service" json:"service"`
}
CreateOutput is a convenience struct for callers who want to return an object similar to `ivcap nextflow create`.
type ServiceDescription ¶
type ServiceDescription struct {
Schema string `yaml:"$schema" json:"$schema"`
ID string `yaml:"$id" json:"$id"`
Name string `yaml:"name" json:"name"`
Description string `yaml:"description" json:"description"`
RequestSchema any `yaml:"request-schema" json:"request-schema"`
Contact any `yaml:"contact" json:"contact"`
Policy string `yaml:"policy" json:"policy"`
ControllerSchema string `yaml:"controller-schema" json:"controller-schema"`
Controller any `yaml:"controller" json:"controller"`
}
func BuildServiceDescription ¶
func BuildServiceDescription(tool *ToolHeader, serviceID string, pipelineArtifactURN string) *ServiceDescription
type SimpleProperty ¶
type SimpleToolHeader ¶
type SimpleToolHeader struct {
Schema string `yaml:"$schema" json:"$schema"`
ID string `yaml:"id" json:"id"`
Name string `yaml:"name" json:"name"`
ServiceID string `yaml:"service-id" json:"service-id"`
Description string `yaml:"description" json:"description"`
Contact *struct {
Name string `yaml:"name" json:"name"`
Email string `yaml:"email" json:"email"`
} `yaml:"contact" json:"contact"`
Properties []SimpleProperty `yaml:"properties" json:"properties"`
Samples []SimpleProperty `yaml:"samples" json:"samples"`
Example map[string]any `yaml:"example" json:"example"`
}
type Source ¶
type Source struct {
// Path inside the assembled archive.
Path string `json:"path"`
// One of: text, base64, url, artifact
Type string `json:"type"`
// For text
Text string `json:"text,omitempty"`
// For base64
Base64 string `json:"base64,omitempty"`
// For url
URL string `json:"url,omitempty"`
// For artifact
ArtifactID string `json:"artifact_id,omitempty"`
ArtifactPath string `json:"artifact_path,omitempty"`
// Optional mime type for manifest.
MediaType string `json:"media_type,omitempty"`
}
Source describes a file which should become a file at `Path` inside an assembled Nextflow pipeline tar.gz.
type ToolHeader ¶
type ToolHeader struct {
Schema string `yaml:"$schema" json:"$schema"`
ID string `yaml:"id" json:"id"`
Name string `yaml:"name" json:"name"`
ServiceID string `yaml:"service-id" json:"service-id"`
Description string `yaml:"description" json:"description"`
Contact *struct {
Name string `yaml:"name" json:"name"`
Email string `yaml:"email" json:"email"`
} `yaml:"contact" json:"contact"`
FnSchema map[string]any `yaml:"fn-schema" json:"fn-schema"`
}
func ConvertSimpleToolToToolHeader ¶
func ConvertSimpleToolToToolHeader(simple *SimpleToolHeader) (*ToolHeader, error)
func LoadToolHeaderFromArchiveBytes ¶
func LoadToolHeaderFromArchiveBytes(archive []byte) (*ToolHeader, string, error)
LoadToolHeaderFromArchiveBytes reads ivcap.yaml or ivcap-tool.yaml from a tar/tar.gz archive provided as bytes.
Returns:
- tool header (or nil if not found)
- found path in archive
func LoadToolHeaderFromArchivePath ¶
func LoadToolHeaderFromArchivePath(archivePath string) (*ToolHeader, string, error)
Source Files