Documentation
¶
Index ¶
- Variables
- func WithRegion(ctx context.Context, region string) context.Context
- type AnnotationImportItem
- type AnnotationImportItemDetail
- type AnnotationImportJob
- type AnnotationImportJobSummary
- type AnnotationStore
- type AnnotationStoreSummary
- type AnnotationStoreVersion
- type AnnotationStoreVersionSummary
- type Configuration
- type ConfigurationDetails
- type ConfigurationRunConfigurations
- type ConfigurationVpcConfig
- type CreateAnnotationStoreResponse
- type DefaultRunSetting
- type Handler
- func (h *Handler) ExtractOperation(c *echo.Context) string
- func (h *Handler) ExtractResource(c *echo.Context) string
- func (h *Handler) GetSupportedOperations() []string
- func (h *Handler) Handler() echo.HandlerFunc
- func (h *Handler) MatchPriority() int
- func (h *Handler) Name() string
- func (h *Handler) Reset()
- func (h *Handler) Restore(ctx context.Context, data []byte) error
- func (h *Handler) RouteMatcher() service.Matcher
- func (h *Handler) Snapshot(ctx context.Context) []byte
- type ImportJobFilter
- type InMemoryBackend
- func (b *InMemoryBackend) AbortMultipartReadSetUpload(sequenceStoreID, uploadID string) error
- func (b *InMemoryBackend) AcceptShare(shareID string) (*Share, error)
- func (b *InMemoryBackend) AccountID() string
- func (b *InMemoryBackend) BatchDeleteReadSet(sequenceStoreID string, ids []string) ([]ReadSetBatchError, error)
- func (b *InMemoryBackend) CancelAnnotationImportJob(jobID string) error
- func (b *InMemoryBackend) CancelRun(id string) error
- func (b *InMemoryBackend) CancelRunBatch(id string) error
- func (b *InMemoryBackend) CancelVariantImportJob(jobID string) error
- func (b *InMemoryBackend) CompleteMultipartReadSetUpload(sequenceStoreID, uploadID string) (*ReadSetMetadata, error)
- func (b *InMemoryBackend) CreateAnnotationStore(name, storeFormat string, reference, sseConfig, storeOptions map[string]any, ...) (*AnnotationStore, error)
- func (b *InMemoryBackend) CreateAnnotationStoreVersion(name, versionName, description string, tags map[string]string) (*AnnotationStoreVersion, error)
- func (b *InMemoryBackend) CreateConfiguration(name, description string, runConfigurations *ConfigurationRunConfigurations, ...) (*Configuration, error)
- func (b *InMemoryBackend) CreateMultipartReadSetUpload(...) (*MultipartReadSetUpload, error)
- func (b *InMemoryBackend) CreateReferenceStore(name, description string, tags map[string]string) (*ReferenceStore, error)
- func (b *InMemoryBackend) CreateRunCache(name, cacheS3Location string, tags map[string]string) (*RunCache, error)
- func (b *InMemoryBackend) CreateRunGroup(name string, maxCPUs, maxRuns, maxDuration int, maxGPUs int, ...) (*RunGroup, error)
- func (b *InMemoryBackend) CreateSequenceStore(name, description, eTagAlgorithmFamily, accessLogLocation string, ...) (*SequenceStore, error)
- func (b *InMemoryBackend) CreateShare(resourceARN, principalSubscriber, name string) (*Share, error)
- func (b *InMemoryBackend) CreateVariantStore(name string, reference, sseConfig map[string]any, tags map[string]string) (*VariantStore, error)
- func (b *InMemoryBackend) CreateWorkflow(name, description, _, _, engine string, tags map[string]string) (*Workflow, error)
- func (b *InMemoryBackend) CreateWorkflowVersion(workflowID, versionName, description string, tags map[string]string) (*WorkflowVersion, error)
- func (b *InMemoryBackend) DeleteAnnotationStore(name string) (*AnnotationStore, error)
- func (b *InMemoryBackend) DeleteAnnotationStoreVersions(name string, versionNames []string) ([]VersionDeleteError, error)
- func (b *InMemoryBackend) DeleteConfiguration(name string) error
- func (b *InMemoryBackend) DeleteReference(referenceStoreID, id string) error
- func (b *InMemoryBackend) DeleteReferenceStore(id string) error
- func (b *InMemoryBackend) DeleteRun(id string) error
- func (b *InMemoryBackend) DeleteRunBatch(id string) error
- func (b *InMemoryBackend) DeleteRunCache(id string) error
- func (b *InMemoryBackend) DeleteRunGroup(id string) error
- func (b *InMemoryBackend) DeleteRunsInBatch(batchID string) error
- func (b *InMemoryBackend) DeleteS3AccessPolicy(s3AccessPointARN string) error
- func (b *InMemoryBackend) DeleteSequenceStore(id string) error
- func (b *InMemoryBackend) DeleteShare(shareID string) (*Share, error)
- func (b *InMemoryBackend) DeleteVariantStore(name string) (*VariantStore, error)
- func (b *InMemoryBackend) DeleteWorkflow(id string) error
- func (b *InMemoryBackend) DeleteWorkflowVersion(workflowID, versionName string) error
- func (b *InMemoryBackend) GetAnnotationImportJob(jobID string) (*AnnotationImportJob, error)
- func (b *InMemoryBackend) GetAnnotationStore(name string) (*AnnotationStore, error)
- func (b *InMemoryBackend) GetAnnotationStoreVersion(name, versionName string) (*AnnotationStoreVersion, error)
- func (b *InMemoryBackend) GetConfiguration(name string) (*Configuration, error)
- func (b *InMemoryBackend) GetReadSetActivationJob(sequenceStoreID, jobID string) (*ReadSetActivationJob, error)
- func (b *InMemoryBackend) GetReadSetBytes(sequenceStoreID, id string) ([]byte, error)
- func (b *InMemoryBackend) GetReadSetExportJob(sequenceStoreID, jobID string) (*ReadSetExportJob, error)
- func (b *InMemoryBackend) GetReadSetImportJob(sequenceStoreID, jobID string) (*ReadSetImportJob, error)
- func (b *InMemoryBackend) GetReadSetMetadata(sequenceStoreID, id string) (*ReadSetMetadata, error)
- func (b *InMemoryBackend) GetReferenceBytes(referenceStoreID, id string) ([]byte, error)
- func (b *InMemoryBackend) GetReferenceImportJob(referenceStoreID, jobID string) (*ReferenceImportJob, error)
- func (b *InMemoryBackend) GetReferenceMetadata(referenceStoreID, id string) (*ReferenceMetadata, error)
- func (b *InMemoryBackend) GetReferenceStore(id string) (*ReferenceStore, error)
- func (b *InMemoryBackend) GetRun(id string) (*Run, error)
- func (b *InMemoryBackend) GetRunBatch(id string) (*RunBatch, error)
- func (b *InMemoryBackend) GetRunBatchSummary(id string) (RunBatchSummary, error)
- func (b *InMemoryBackend) GetRunCache(id string) (*RunCache, error)
- func (b *InMemoryBackend) GetRunGroup(id string) (*RunGroup, error)
- func (b *InMemoryBackend) GetRunTask(runID, taskID string) (*RunTask, error)
- func (b *InMemoryBackend) GetS3AccessPolicy(s3AccessPointARN string) (*S3AccessPolicy, error)
- func (b *InMemoryBackend) GetSequenceStore(id string) (*SequenceStore, error)
- func (b *InMemoryBackend) GetShare(shareID string) (*Share, error)
- func (b *InMemoryBackend) GetVariantImportJob(jobID string) (*VariantImportJob, error)
- func (b *InMemoryBackend) GetVariantStore(name string) (*VariantStore, error)
- func (b *InMemoryBackend) GetWorkflow(id string) (*Workflow, error)
- func (b *InMemoryBackend) GetWorkflowVersion(workflowID, versionName string) (*WorkflowVersion, error)
- func (b *InMemoryBackend) ListAnnotationImportJobs(filter *ImportJobFilter, ids0 []string, maxResults int, nextToken string) ([]*AnnotationImportJob, string, error)
- func (b *InMemoryBackend) ListAnnotationStoreVersions(name string, filter *StoreStatusFilter, maxResults int, nextToken string) ([]*AnnotationStoreVersion, string, error)
- func (b *InMemoryBackend) ListAnnotationStores(filter *StoreStatusFilter, ids0 []string, maxResults int, nextToken string) ([]*AnnotationStore, string, error)
- func (b *InMemoryBackend) ListConfigurations(maxResults int, nextToken string) ([]*Configuration, string, error)
- func (b *InMemoryBackend) ListMultipartReadSetUploads(sequenceStoreID string, maxResults int, nextToken string) ([]*MultipartReadSetUpload, string, error)
- func (b *InMemoryBackend) ListReadSetActivationJobs(sequenceStoreID string, maxResults int, nextToken string) ([]*ReadSetActivationJob, string, error)
- func (b *InMemoryBackend) ListReadSetExportJobs(sequenceStoreID string, maxResults int, nextToken string) ([]*ReadSetExportJob, string, error)
- func (b *InMemoryBackend) ListReadSetImportJobs(sequenceStoreID string, maxResults int, nextToken string) ([]*ReadSetImportJob, string, error)
- func (b *InMemoryBackend) ListReadSetUploadParts(sequenceStoreID, uploadID string, maxResults int, nextToken string) ([]*ReadSetUploadPart, string, error)
- func (b *InMemoryBackend) ListReadSets(sequenceStoreID string, filter *ReadSetFilter, maxResults int, ...) ([]*ReadSetMetadata, string, error)
- func (b *InMemoryBackend) ListReferenceImportJobs(referenceStoreID string, filter *ReferenceImportJobFilter, maxResults int, ...) ([]*ReferenceImportJob, string, error)
- func (b *InMemoryBackend) ListReferenceStores(filter *ReferenceStoreFilter, maxResults int, nextToken string) ([]*ReferenceStore, string, error)
- func (b *InMemoryBackend) ListReferences(referenceStoreID string, filter *ReferenceFilter, maxResults int, ...) ([]*ReferenceMetadata, string, error)
- func (b *InMemoryBackend) ListRunBatches(filter *RunBatchFilter, maxResults int, nextToken string) ([]*RunBatch, string, error)
- func (b *InMemoryBackend) ListRunCaches(maxResults int, nextToken string) ([]*RunCache, string, error)
- func (b *InMemoryBackend) ListRunGroups(filter *RunGroupFilter, maxResults int, nextToken string) ([]*RunGroup, string, error)
- func (b *InMemoryBackend) ListRunTasks(runID string, filter *RunTaskFilter, maxResults int, nextToken string) ([]*RunTask, string, error)
- func (b *InMemoryBackend) ListRuns(filter *RunFilter, maxResults int, nextToken string) ([]*Run, string, error)
- func (b *InMemoryBackend) ListRunsInBatch(batchID string, filter *RunsInBatchFilter, maxResults int, nextToken string) ([]*Run, string, error)
- func (b *InMemoryBackend) ListSequenceStores(filter *SequenceStoreFilter, maxResults int, nextToken string) ([]*SequenceStore, string, error)
- func (b *InMemoryBackend) ListShares(resourceOwner string, filter *ShareFilter, maxResults int, nextToken string) ([]*Share, string, error)
- func (b *InMemoryBackend) ListTagsForResource(resourceARN string) (map[string]string, error)
- func (b *InMemoryBackend) ListVariantImportJobs(filter *ImportJobFilter, ids0 []string, maxResults int, nextToken string) ([]*VariantImportJob, string, error)
- func (b *InMemoryBackend) ListVariantStores(filter *StoreStatusFilter, ids0 []string, maxResults int, nextToken string) ([]*VariantStore, string, error)
- func (b *InMemoryBackend) ListWorkflowVersions(workflowID string, filter *WorkflowVersionFilter, maxResults int, ...) ([]*WorkflowVersion, string, error)
- func (b *InMemoryBackend) ListWorkflows(filter *WorkflowFilter, maxResults int, nextToken string) ([]*Workflow, string, error)
- func (b *InMemoryBackend) PutS3AccessPolicy(s3AccessPointARN, policy string) error
- func (b *InMemoryBackend) Region() string
- func (b *InMemoryBackend) Reset()
- func (b *InMemoryBackend) Restore(ctx context.Context, data []byte) error
- func (b *InMemoryBackend) Snapshot(ctx context.Context) []byte
- func (b *InMemoryBackend) StartAnnotationImportJob(destinationName, roleARN string, items []AnnotationImportItem, ...) (*AnnotationImportJob, error)
- func (b *InMemoryBackend) StartReadSetActivationJob(sequenceStoreID string, sources []ReadSetActivationJobSource) (*ReadSetActivationJob, error)
- func (b *InMemoryBackend) StartReadSetExportJob(sequenceStoreID, destination string, sources []ReadSetExportJobSource) (*ReadSetExportJob, error)
- func (b *InMemoryBackend) StartReadSetImportJob(sequenceStoreID, roleARN string, sources []ReadSetImportJobSource) (*ReadSetImportJob, error)
- func (b *InMemoryBackend) StartReferenceImportJob(referenceStoreID, roleARN string, sources []ReferenceImportJobSource) (*ReferenceImportJob, error)
- func (b *InMemoryBackend) StartRun(workflowID, roleARN, name, runGroupID, runBatchID, networkingMode, ... string, ...) (*Run, error)
- func (b *InMemoryBackend) StartRunBatch(batchName string, def DefaultRunSetting, inlineSettings []InlineRunSetting, ...) (*RunBatch, error)
- func (b *InMemoryBackend) StartVariantImportJob(destinationName, roleARN string, items []VariantImportItem, ...) (*VariantImportJob, error)
- func (b *InMemoryBackend) TagResource(resourceARN string, tags map[string]string) error
- func (b *InMemoryBackend) UntagResource(resourceARN string, tagKeys []string) error
- func (b *InMemoryBackend) UpdateAnnotationStore(name, description string) (*AnnotationStore, error)
- func (b *InMemoryBackend) UpdateAnnotationStoreVersion(name, versionName, description string) (*AnnotationStoreVersion, error)
- func (b *InMemoryBackend) UpdateRunCache(id, name, description string) error
- func (b *InMemoryBackend) UpdateRunGroup(id, name string, maxCPUs, maxRuns, maxDuration int, maxGPUs int) (*RunGroup, error)
- func (b *InMemoryBackend) UpdateSequenceStore(id, name, description string) (*SequenceStore, error)
- func (b *InMemoryBackend) UpdateVariantStore(name, description string) (*VariantStore, error)
- func (b *InMemoryBackend) UpdateWorkflow(id, name, description string) error
- func (b *InMemoryBackend) UpdateWorkflowVersion(workflowID, versionName, description string) error
- func (b *InMemoryBackend) UploadReadSetPart(sequenceStoreID, uploadID string, partNumber int, partSource string, ...) (string, error)
- type InlineRunSetting
- type MultipartReadSetUpload
- type Provider
- type ReadSetActivationJob
- type ReadSetActivationJobSource
- type ReadSetBatchError
- type ReadSetExportJob
- type ReadSetExportJobSource
- type ReadSetFilter
- type ReadSetImportJob
- type ReadSetImportJobSource
- type ReadSetMetadata
- type ReadSetUploadPart
- type ReferenceFilter
- type ReferenceImportJob
- type ReferenceImportJobFilter
- type ReferenceImportJobSource
- type ReferenceMetadata
- type ReferenceStore
- type ReferenceStoreFilter
- type Run
- type RunBatch
- type RunBatchFilter
- type RunBatchSummary
- type RunCache
- type RunFilter
- type RunGroup
- type RunGroupFilter
- type RunTask
- type RunTaskFilter
- type RunsInBatchFilter
- type S3AccessPolicy
- type SequenceStore
- type SequenceStoreFilter
- type Share
- type ShareFilter
- type StorageBackend
- type StoreStatusFilter
- type VariantImportItem
- type VariantImportItemDetail
- type VariantImportJob
- type VariantImportJobSummary
- type VariantStore
- type VariantStoreSummary
- type VersionDeleteError
- type Workflow
- type WorkflowFilter
- type WorkflowVersion
- type WorkflowVersionFilter
Constants ¶
This section is empty.
Variables ¶
var ( // ErrNotFound is returned when a resource does not exist. ErrNotFound = awserr.New(errResourceNotFound, awserr.ErrNotFound) // ErrAlreadyExists is returned when a resource already exists. ErrAlreadyExists = awserr.New(errConflict, awserr.ErrAlreadyExists) // ErrValidation is returned on invalid input. ErrValidation = awserr.New(errValidation, awserr.ErrInvalidParameter) // ErrInvalidState is returned when a resource is not in the state // required for the requested operation (e.g. deleting a RunBatch that // hasn't reached a terminal status). ErrInvalidState = awserr.New(errConflict, awserr.ErrConflict) )
var ErrNilAppContext = errors.New("omics: nil app context")
ErrNilAppContext is returned when Init is called with a nil AppContext.
Functions ¶
Types ¶
type AnnotationImportItem ¶
type AnnotationImportItem struct {
Source string `json:"source"`
}
AnnotationImportItem is a source item for an annotation import job -- real types.AnnotationImportItemSource (types.go:91-99, omics@v1.49.5): Source only. This is StartAnnotationImportJobInput.Items' element shape, not the response shape GetAnnotationImportJobOutput.Items uses (see AnnotationImportItemDetail) -- the two are declared separately below rather than one struct serving both, the same trap the ID/jobId field already forced apart for this job type (c41d36cb6).
type AnnotationImportItemDetail ¶ added in v1.3.1
type AnnotationImportItemDetail struct {
JobStatus string `json:"jobStatus"`
Source string `json:"source"`
}
AnnotationImportItemDetail is the real GetAnnotationImportJobOutput.Items element, types.AnnotationImportItemDetail (types.go:75-89): JobStatus and Source, both required. JobStatus is set once from the job's own Status at Start time (annotationImportItemDetails, annotation_stores.go): this backend completes import jobs synchronously in one step, so every item reaches its final status in that same step and there is no async window in which a stored per-item value could go stale.
gopherstack-7s8r assumed ListAnnotationImportJobs also returns this shape; it does not -- the real List element (AnnotationImportJobItem, types.go:102-146) has no Items field at all. See AnnotationImportJobSummary.
type AnnotationImportJob ¶
type AnnotationImportJob struct {
CreationTime time.Time `json:"creationTime"`
CompletionTime *time.Time `json:"completionTime,omitempty"`
UpdateTime time.Time `json:"updateTime"`
FormatOptions map[string]any `json:"formatOptions,omitempty"`
AnnotationFields map[string]string `json:"annotationFields,omitempty"`
ID string `json:"id"`
DestinationName string `json:"destinationName"`
RoleARN string `json:"roleArn"`
Status string `json:"status"`
StatusMessage string `json:"statusMessage"`
VersionName string `json:"versionName"`
Items []AnnotationImportItemDetail `json:"items"`
RunLeftNormalization bool `json:"runLeftNormalization,omitempty"`
}
AnnotationImportJob is the real GetAnnotationImportJobOutput shape (deserializers.go:5949-6015) and this backend's persisted job record.
ID is tagged "id" -- the real GetAnnotationImportJobOutput/ AnnotationImportJobItem wire key (deserializers.go:5954) -- which is right for Get/List but wrong for StartAnnotationImportJobOutput, whose only field is "jobId" (deserializers.go:17434); the two ops don't share a response shape in the real API, so the start handler builds its own {"jobId": ...} response instead of marshaling this struct. ListAnnotationImportJobs doesn't marshal this struct either -- see AnnotationImportJobSummary.
FormatOptions/RunLeftNormalization/VersionName/StatusMessage/UpdateTime are real required GetAnnotationImportJobOutput members (deserializers.go:5949- 6015) that were previously absent from this struct entirely -- a schema gap, not a dropped key. FormatOptions mirrors the Reference/SseConfig/ StoreOptions convention (passthrough map, real shape is a tagged union of tsvOptions/vcfOptions). StatusMessage is always empty: this backend completes import jobs synchronously with no error state to describe.
type AnnotationImportJobSummary ¶ added in v1.3.1
type AnnotationImportJobSummary struct {
CreationTime time.Time `json:"creationTime"`
CompletionTime *time.Time `json:"completionTime,omitempty"`
UpdateTime time.Time `json:"updateTime"`
AnnotationFields map[string]string `json:"annotationFields,omitempty"`
ID string `json:"id"`
DestinationName string `json:"destinationName"`
RoleARN string `json:"roleArn"`
Status string `json:"status"`
VersionName string `json:"versionName"`
RunLeftNormalization bool `json:"runLeftNormalization,omitempty"`
}
AnnotationImportJobSummary is the real ListAnnotationImportJobsOutput element, types.AnnotationImportJobItem (types.go:102-146). It is deliberately narrower than AnnotationImportJob/GetAnnotationImportJobOutput: no Items, FormatOptions or StatusMessage -- List and Get are not the same response shape in the real API, the same class of gap that already forced StartAnnotationImportJobOutput apart to a standalone {"jobId": ...} body.
type AnnotationStore ¶
type AnnotationStore struct {
CreationTime time.Time `json:"creationTime"`
UpdateTime time.Time `json:"updateTime"`
Reference map[string]any `json:"reference,omitempty"`
SseConfig map[string]any `json:"sseConfig,omitempty"`
StoreOptions map[string]any `json:"storeOptions,omitempty"`
Tags map[string]string `json:"tags"`
StoreArn string `json:"storeArn"`
ID string `json:"id"`
Name string `json:"name"`
Description string `json:"description"`
StoreFormat string `json:"storeFormat"`
Status string `json:"status"`
// StatusMessage is real GetAnnotationStoreOutput's required
// "statusMessage" (deserializers.go, GetAnnotationStore/
// ListAnnotationStores) -- previously absent from this struct entirely,
// the same gap fixed for import jobs in c41d36cb6 but missed here.
// Always empty: this backend transitions store status synchronously
// with no error state to describe.
StatusMessage string `json:"statusMessage"`
// NumVersions is real GetAnnotationStoreOutput's required "numVersions"
// (deserializers.go:6225) -- computed live from annotationVersionsByStore
// at read time (GetAnnotationStore/ListAnnotationStores), never stored,
// since a stored counter would drift as versions are added/deleted.
NumVersions int32 `json:"numVersions"`
// StoreSizeBytes is real GetAnnotationStoreOutput's required
// "storeSizeBytes" (deserializers.go:6289). This backend does not track
// actual stored bytes -- always 0 rather than a fabricated number.
StoreSizeBytes int64 `json:"storeSizeBytes"`
// contains filtered or unexported fields
}
AnnotationStore represents an HealthOmics annotation store.
StoreArn is real GetAnnotationStoreOutput/AnnotationStoreItem wire key "storeArn" (omics@v1.49.5 deserializers.go:6266) -- this struct previously tagged it "arn", a key no real Get/ListAnnotationStores deserializer reads.
type AnnotationStoreSummary ¶ added in v1.3.1
type AnnotationStoreSummary struct {
CreationTime time.Time `json:"creationTime"`
UpdateTime time.Time `json:"updateTime"`
Reference map[string]any `json:"reference,omitempty"`
SseConfig map[string]any `json:"sseConfig,omitempty"`
StoreArn string `json:"storeArn"`
ID string `json:"id"`
Name string `json:"name"`
Description string `json:"description"`
StoreFormat string `json:"storeFormat"`
Status string `json:"status"`
StatusMessage string `json:"statusMessage"`
StoreSizeBytes int64 `json:"storeSizeBytes"`
}
AnnotationStoreSummary is the real ListAnnotationStoresOutput element shape (types.AnnotationStoreItem, omics@v1.49.5 types.go:152-211) -- narrower than GetAnnotationStoreOutput: no numVersions, storeOptions or tags. ListAnnotationStores previously marshaled AnnotationStore directly, leaking all three (gopherstack-dv4s).
type AnnotationStoreVersion ¶
type AnnotationStoreVersion struct {
CreationTime time.Time `json:"creationTime"`
UpdateTime time.Time `json:"updateTime"`
Tags map[string]string `json:"tags"`
VersionArn string `json:"versionArn"`
ID string `json:"id"`
StoreID string `json:"storeId"`
StoreName string `json:"name"`
VersionName string `json:"versionName"`
Description string `json:"description"`
Status string `json:"status"`
// StatusMessage is real GetAnnotationStoreVersionOutput's required
// "statusMessage" -- previously absent from this struct entirely, the
// same gap fixed for import jobs in c41d36cb6 but missed here. Always
// empty: this backend transitions version status synchronously with no
// error state to describe.
StatusMessage string `json:"statusMessage"`
// VersionSizeBytes is real GetAnnotationStoreVersionOutput's required
// "versionSizeBytes" (deserializers.go:6587). This backend does not
// track actual stored bytes -- always 0 rather than a fabricated number.
VersionSizeBytes int64 `json:"versionSizeBytes"`
}
AnnotationStoreVersion represents a version of an annotation store.
VersionArn is real GetAnnotationStoreVersionOutput/AnnotationStoreVersionItem wire key "versionArn" (omics@v1.49.5 deserializers.go:6564) -- this struct previously tagged it "arn", a key no real deserializer for this shape reads.
ID and StoreName's tag are both gopherstack-r80d (batch 7) fixes: Get/Update/CreateAnnotationStoreVersionOutput each require a distinct "id" (the version's own generated ID, api_op_GetAnnotationStoreVersion.go:15-17, deserializers.go:6501) and "name" (the parent store's name, api_op_GetAnnotationStoreVersion.go:19-21, deserializers.go:6510) that this struct never tracked at all -- StoreName held the right value but the wrong wire key ("storeName", a key no real deserializer for this shape reads), and no field existed for "id" at all. Flagged but deliberately left unfixed by two prior passes (lx5h/kb66, dv4s) as "the opposite class" from what those passes targeted; this is exactly gopherstack-r80d's cut.
type AnnotationStoreVersionSummary ¶ added in v1.3.1
type AnnotationStoreVersionSummary struct {
CreationTime time.Time `json:"creationTime"`
UpdateTime time.Time `json:"updateTime"`
VersionArn string `json:"versionArn"`
ID string `json:"id"`
StoreID string `json:"storeId"`
StoreName string `json:"name"`
VersionName string `json:"versionName"`
Description string `json:"description"`
Status string `json:"status"`
StatusMessage string `json:"statusMessage"`
VersionSizeBytes int64 `json:"versionSizeBytes"`
}
AnnotationStoreVersionSummary is the real ListAnnotationStoreVersionsOutput element shape (types.AnnotationStoreVersionItem, omics@v1.49.5 types.go): narrower than GetAnnotationStoreVersionOutput -- no tags.
ID/StoreName ARE real AnnotationStoreVersionItem members too (required "id"/"name", same as Get -- see AnnotationStoreVersion's doc comment); gopherstack-dv4s's note that this type "has no storeName member" was about AnnotationStoreVersion.StoreName's WRONG tag of the time ("storeName", not a real key on any shape), not about the real "name" member being absent from List -- List genuinely has it too, fixed here (gopherstack-r80d batch 7) alongside the identical Get/Update/Create gap.
type Configuration ¶
type Configuration struct {
CreationTime time.Time `json:"creationTime"`
RunConfigurations *ConfigurationRunConfigurations `json:"runConfigurations,omitempty"`
Tags map[string]string `json:"tags,omitempty"`
Name string `json:"name"`
Description string `json:"description,omitempty"`
ARN string `json:"arn,omitempty"`
UUID string `json:"uuid,omitempty"`
Status string `json:"status,omitempty"`
}
Configuration represents an HealthOmics configuration.
type ConfigurationDetails ¶ added in v1.2.0
type ConfigurationDetails struct {
Arn string `json:"arn,omitempty"`
Name string `json:"name,omitempty"`
UUID string `json:"uuid,omitempty"`
}
ConfigurationDetails describes the configuration used for a workflow run (real AWS ConfigurationDetails: arn/name/uuid of the Configuration used).
type ConfigurationRunConfigurations ¶ added in v1.3.1
type ConfigurationRunConfigurations struct {
VpcConfig *ConfigurationVpcConfig `json:"vpcConfig,omitempty"`
}
ConfigurationRunConfigurations mirrors types.RunConfigurations (request) and types.RunConfigurationsResponse (response) (types.go:1523/1532).
type ConfigurationVpcConfig ¶ added in v1.3.1
type ConfigurationVpcConfig struct {
VpcID string `json:"vpcId,omitempty"`
SecurityGroupIDs []string `json:"securityGroupIds,omitempty"`
SubnetIDs []string `json:"subnetIds,omitempty"`
}
ConfigurationVpcConfig mirrors types.VpcConfig on the request side and types.VpcConfigResponse on the response side (types.go:2242/2254) -- both wire shapes share the same field set here. VpcID is the response-only "computed from the provided subnet IDs" field; left empty rather than fabricated since this backend does no real VPC/subnet resolution.
type CreateAnnotationStoreResponse ¶ added in v1.5.0
type CreateAnnotationStoreResponse struct {
CreationTime time.Time `json:"creationTime"`
ID string `json:"id"`
Name string `json:"name"`
Status string `json:"status"`
VersionName string `json:"versionName"`
}
CreateAnnotationStoreResponse is the real CreateAnnotationStoreOutput shape (omics@v1.49.5 api_op_CreateAnnotationStore.go:68-95) -- narrower than AnnotationStore (no description/reference/sseConfig/storeArn/storeFormat/ storeOptions/tags/updateTime/numVersions/storeSizeBytes/statusMessage) and with one member the domain struct never tracked at all: VersionName, real required "versionName" (deserializers.go:1290, CreateAnnotationStore's own deserializer -- distinct from GetAnnotationStoreOutput, which has no such member). Echoes the caller-supplied CreateAnnotationStoreInput.VersionName (also real, optional, api_op_CreateAnnotationStore.go:61-62) verbatim; left empty rather than fabricated when the caller didn't supply one.
type DefaultRunSetting ¶ added in v1.3.1
type DefaultRunSetting struct {
RunTags map[string]string
RoleARN string
WorkflowID string
Name string
OutputURI string
RunGroupID string
Priority int32
}
DefaultRunSetting is the shared configuration StartRunBatch applies to every run in the batch (real types.DefaultRunSetting). Only the subset of fields this backend's StartRun already models is accepted -- see the RunBatch family note in PARITY.md for the rest (CacheBehavior/CacheId/ConfigurationName/EngineSettings/LogLevel/ NetworkingMode/OutputBucketOwnerId/Parameters/RetentionMode/ScratchStorageMode/ StorageCapacity/StorageType/WorkflowOwnerId), which are accepted on the wire but not wired to real behavior.
type Handler ¶
type Handler struct {
Backend StorageBackend
}
Handler handles HealthOmics HTTP requests.
func (*Handler) ExtractOperation ¶
ExtractOperation extracts the operation from the request.
func (*Handler) ExtractResource ¶
ExtractResource extracts the resource identifier.
func (*Handler) GetSupportedOperations ¶
GetSupportedOperations returns all supported operation names, derived from the same opDispatch table handleREST dispatches through -- the two can never drift out of sync.
func (*Handler) Handler ¶
func (h *Handler) Handler() echo.HandlerFunc
Handler returns the Echo handler function.
func (*Handler) MatchPriority ¶
MatchPriority returns the routing priority.
func (*Handler) RouteMatcher ¶
RouteMatcher returns a matcher for HealthOmics REST paths.
type ImportJobFilter ¶ added in v1.2.0
ImportJobFilter is filter criteria shared by ListAnnotationImportJobs and ListVariantImportJobs (status + owning store name).
type InMemoryBackend ¶
type InMemoryBackend struct {
// contains filtered or unexported fields
}
InMemoryBackend is the in-memory backend for HealthOmics.
Every resource collection that carries its own identity field (ID, Name, or ShareID) is a directly keyed store.Table; every collection that was previously nested by a parent store/workflow/run/annotation-store is a store.Table keyed by the composite "parent|id" string (see parentKey), with a companion store.Index grouping entries by parent for per-parent scans -- the same pattern services/emr and services/codeartifact use for their region-nested resources. HealthOmics's "region" dimension itself was never actually exercised (every pre-refactor call site read/wrote b.region(b.defaultRegion) only -- WithRegion's context value never reached a lookup), so unlike emr/codeartifact no region qualifier is threaded through these keys; only the genuine parent/child nesting is preserved.
uploadParts (order-sensitive: part listing walks it in append order, not sorted order), uploadPartData/readSetBytes/referenceBytes (raw []byte values, not *V), and tags (map[string]string values, not *V) are not eligible for store.Table and remain plain nested maps. Field order below is deliberate: it was determined by running fieldalignment -fix on an isolated scratch copy of this struct (never directly on this package -- see the fieldalignment hazard note in .claude/memories/parity-principles.md-adjacent process docs) and then hand-applied here. It shaves 8 pointer-bytes of padding off the struct; do not reorder without re-checking on a scratch copy.
func NewInMemoryBackend ¶
func NewInMemoryBackend(accountID, region string) *InMemoryBackend
NewInMemoryBackend creates a new InMemoryBackend.
func (*InMemoryBackend) AbortMultipartReadSetUpload ¶
func (b *InMemoryBackend) AbortMultipartReadSetUpload(sequenceStoreID, uploadID string) error
AbortMultipartReadSetUpload aborts a multipart read set upload.
func (*InMemoryBackend) AcceptShare ¶
func (b *InMemoryBackend) AcceptShare(shareID string) (*Share, error)
AcceptShare accepts a share invitation.
func (*InMemoryBackend) AccountID ¶
func (b *InMemoryBackend) AccountID() string
AccountID returns the account ID.
func (*InMemoryBackend) BatchDeleteReadSet ¶
func (b *InMemoryBackend) BatchDeleteReadSet( sequenceStoreID string, ids []string, ) ([]ReadSetBatchError, error)
BatchDeleteReadSet deletes multiple read sets.
func (*InMemoryBackend) CancelAnnotationImportJob ¶
func (b *InMemoryBackend) CancelAnnotationImportJob(jobID string) error
CancelAnnotationImportJob cancels an annotation import job.
func (*InMemoryBackend) CancelRun ¶
func (b *InMemoryBackend) CancelRun(id string) error
CancelRun cancels a run.
func (*InMemoryBackend) CancelRunBatch ¶
func (b *InMemoryBackend) CancelRunBatch(id string) error
CancelRunBatch cancels a run batch.
func (*InMemoryBackend) CancelVariantImportJob ¶
func (b *InMemoryBackend) CancelVariantImportJob(jobID string) error
CancelVariantImportJob cancels a variant import job.
func (*InMemoryBackend) CompleteMultipartReadSetUpload ¶
func (b *InMemoryBackend) CompleteMultipartReadSetUpload( sequenceStoreID, uploadID string, ) (*ReadSetMetadata, error)
CompleteMultipartReadSetUpload completes a multipart read set upload.
func (*InMemoryBackend) CreateAnnotationStore ¶
func (b *InMemoryBackend) CreateAnnotationStore( name, storeFormat string, reference, sseConfig, storeOptions map[string]any, tags map[string]string, ) (*AnnotationStore, error)
CreateAnnotationStore creates a new annotation store.
func (*InMemoryBackend) CreateAnnotationStoreVersion ¶
func (b *InMemoryBackend) CreateAnnotationStoreVersion( name, versionName, description string, tags map[string]string, ) (*AnnotationStoreVersion, error)
CreateAnnotationStoreVersion creates a version of an annotation store.
func (*InMemoryBackend) CreateConfiguration ¶
func (b *InMemoryBackend) CreateConfiguration( name, description string, runConfigurations *ConfigurationRunConfigurations, tags map[string]string, ) (*Configuration, error)
CreateConfiguration creates a configuration. runConfigurations is a required CreateConfigurationInput member (verified against validateOpCreateConfigurationInput, validators.go) that the pre-fix request never read at all.
func (*InMemoryBackend) CreateMultipartReadSetUpload ¶
func (b *InMemoryBackend) CreateMultipartReadSetUpload( sequenceStoreID, name, sourceFileType, sampleID, subjectID, generatedFrom, referenceARN, description string, tags map[string]string, ) (*MultipartReadSetUpload, error)
CreateMultipartReadSetUpload creates a multipart read set upload.
func (*InMemoryBackend) CreateReferenceStore ¶
func (b *InMemoryBackend) CreateReferenceStore( name, description string, tags map[string]string, ) (*ReferenceStore, error)
CreateReferenceStore creates a new reference store.
func (*InMemoryBackend) CreateRunCache ¶
func (b *InMemoryBackend) CreateRunCache( name, cacheS3Location string, tags map[string]string, ) (*RunCache, error)
CreateRunCache creates a new run cache.
func (*InMemoryBackend) CreateRunGroup ¶
func (b *InMemoryBackend) CreateRunGroup( name string, maxCPUs, maxRuns, maxDuration int, maxGPUs int, tags map[string]string, ) (*RunGroup, error)
CreateRunGroup creates a new run group.
func (*InMemoryBackend) CreateSequenceStore ¶
func (b *InMemoryBackend) CreateSequenceStore( name, description, eTagAlgorithmFamily, accessLogLocation string, tags map[string]string, ) (*SequenceStore, error)
CreateSequenceStore creates a new sequence store.
func (*InMemoryBackend) CreateShare ¶
func (b *InMemoryBackend) CreateShare( resourceARN, principalSubscriber, name string, ) (*Share, error)
CreateShare creates a new resource share.
func (*InMemoryBackend) CreateVariantStore ¶
func (b *InMemoryBackend) CreateVariantStore( name string, reference, sseConfig map[string]any, tags map[string]string, ) (*VariantStore, error)
CreateVariantStore creates a new variant store.
sseConfig is real CreateVariantStoreInput's optional "sseConfig" (api_op_CreateVariantStore.go) -- previously not even read by the handler, despite GetVariantStoreOutput/VariantStoreItem requiring it on every response (types.go); the same passthrough-map convention AnnotationStore already uses (gopherstack-r80d batch 7).
func (*InMemoryBackend) CreateWorkflow ¶
func (b *InMemoryBackend) CreateWorkflow( name, description, _, _, engine string, tags map[string]string, ) (*Workflow, error)
CreateWorkflow creates a new workflow.
func (*InMemoryBackend) CreateWorkflowVersion ¶
func (b *InMemoryBackend) CreateWorkflowVersion( workflowID, versionName, description string, tags map[string]string, ) (*WorkflowVersion, error)
CreateWorkflowVersion creates a new workflow version.
func (*InMemoryBackend) DeleteAnnotationStore ¶
func (b *InMemoryBackend) DeleteAnnotationStore(name string) (*AnnotationStore, error)
DeleteAnnotationStore deletes an annotation store.
func (*InMemoryBackend) DeleteAnnotationStoreVersions ¶
func (b *InMemoryBackend) DeleteAnnotationStoreVersions( name string, versionNames []string, ) ([]VersionDeleteError, error)
DeleteAnnotationStoreVersions deletes one or more annotation store versions.
func (*InMemoryBackend) DeleteConfiguration ¶
func (b *InMemoryBackend) DeleteConfiguration(name string) error
DeleteConfiguration deletes a configuration.
func (*InMemoryBackend) DeleteReference ¶
func (b *InMemoryBackend) DeleteReference(referenceStoreID, id string) error
DeleteReference deletes a reference by store ID and reference ID.
func (*InMemoryBackend) DeleteReferenceStore ¶
func (b *InMemoryBackend) DeleteReferenceStore(id string) error
DeleteReferenceStore deletes a reference store by ID.
func (*InMemoryBackend) DeleteRun ¶
func (b *InMemoryBackend) DeleteRun(id string) error
DeleteRun deletes a run.
func (*InMemoryBackend) DeleteRunBatch ¶
func (b *InMemoryBackend) DeleteRunBatch(id string) error
DeleteRunBatch deletes a single run batch resource (real AWS DeleteBatch semantics). Real AWS requires the batch to already be in a terminal state (PROCESSED/FAILED/CANCELLED/RUNS_DELETED) before it will delete the batch metadata; attempting to delete a batch still in progress returns a ConflictException.
func (*InMemoryBackend) DeleteRunCache ¶
func (b *InMemoryBackend) DeleteRunCache(id string) error
DeleteRunCache deletes a run cache.
func (*InMemoryBackend) DeleteRunGroup ¶
func (b *InMemoryBackend) DeleteRunGroup(id string) error
DeleteRunGroup deletes a run group.
func (*InMemoryBackend) DeleteRunsInBatch ¶
func (b *InMemoryBackend) DeleteRunsInBatch(batchID string) error
DeleteRunsInBatch deletes the individual workflow runs that belong to a run batch (real DeleteRunBatch semantics: POST /runBatch/delete with a single batchId in the body). The run batch resource itself is left intact; use DeleteRunBatch (DELETE /runBatch/{batchId}, real DeleteBatch semantics) to remove the batch metadata afterward.
func (*InMemoryBackend) DeleteS3AccessPolicy ¶
func (b *InMemoryBackend) DeleteS3AccessPolicy(s3AccessPointARN string) error
DeleteS3AccessPolicy deletes an S3 access policy.
func (*InMemoryBackend) DeleteSequenceStore ¶
func (b *InMemoryBackend) DeleteSequenceStore(id string) error
DeleteSequenceStore deletes a sequence store by ID.
func (*InMemoryBackend) DeleteShare ¶
func (b *InMemoryBackend) DeleteShare(shareID string) (*Share, error)
DeleteShare deletes a share.
func (*InMemoryBackend) DeleteVariantStore ¶
func (b *InMemoryBackend) DeleteVariantStore(name string) (*VariantStore, error)
DeleteVariantStore deletes a variant store.
func (*InMemoryBackend) DeleteWorkflow ¶
func (b *InMemoryBackend) DeleteWorkflow(id string) error
DeleteWorkflow deletes a workflow.
func (*InMemoryBackend) DeleteWorkflowVersion ¶
func (b *InMemoryBackend) DeleteWorkflowVersion(workflowID, versionName string) error
DeleteWorkflowVersion deletes a workflow version.
func (*InMemoryBackend) GetAnnotationImportJob ¶
func (b *InMemoryBackend) GetAnnotationImportJob(jobID string) (*AnnotationImportJob, error)
GetAnnotationImportJob retrieves an annotation import job.
func (*InMemoryBackend) GetAnnotationStore ¶
func (b *InMemoryBackend) GetAnnotationStore(name string) (*AnnotationStore, error)
GetAnnotationStore retrieves an annotation store, advancing CREATING→ACTIVE on first poll (real AnnotationStoreCreatedWaiter clients poll until Status == ACTIVE).
func (*InMemoryBackend) GetAnnotationStoreVersion ¶
func (b *InMemoryBackend) GetAnnotationStoreVersion( name, versionName string, ) (*AnnotationStoreVersion, error)
GetAnnotationStoreVersion retrieves an annotation store version.
func (*InMemoryBackend) GetConfiguration ¶
func (b *InMemoryBackend) GetConfiguration(name string) (*Configuration, error)
GetConfiguration retrieves a configuration.
func (*InMemoryBackend) GetReadSetActivationJob ¶
func (b *InMemoryBackend) GetReadSetActivationJob( sequenceStoreID, jobID string, ) (*ReadSetActivationJob, error)
GetReadSetActivationJob retrieves a read set activation job.
func (*InMemoryBackend) GetReadSetBytes ¶
func (b *InMemoryBackend) GetReadSetBytes(sequenceStoreID, id string) ([]byte, error)
GetReadSetBytes returns the stored binary body for a read set.
func (*InMemoryBackend) GetReadSetExportJob ¶
func (b *InMemoryBackend) GetReadSetExportJob( sequenceStoreID, jobID string, ) (*ReadSetExportJob, error)
GetReadSetExportJob retrieves a read set export job.
func (*InMemoryBackend) GetReadSetImportJob ¶
func (b *InMemoryBackend) GetReadSetImportJob( sequenceStoreID, jobID string, ) (*ReadSetImportJob, error)
GetReadSetImportJob retrieves a read set import job.
func (*InMemoryBackend) GetReadSetMetadata ¶
func (b *InMemoryBackend) GetReadSetMetadata(sequenceStoreID, id string) (*ReadSetMetadata, error)
GetReadSetMetadata retrieves read set metadata.
func (*InMemoryBackend) GetReferenceBytes ¶
func (b *InMemoryBackend) GetReferenceBytes(referenceStoreID, id string) ([]byte, error)
GetReferenceBytes returns the stored binary body for a reference.
func (*InMemoryBackend) GetReferenceImportJob ¶
func (b *InMemoryBackend) GetReferenceImportJob( referenceStoreID, jobID string, ) (*ReferenceImportJob, error)
GetReferenceImportJob retrieves a reference import job.
func (*InMemoryBackend) GetReferenceMetadata ¶
func (b *InMemoryBackend) GetReferenceMetadata( referenceStoreID, id string, ) (*ReferenceMetadata, error)
GetReferenceMetadata retrieves reference metadata.
func (*InMemoryBackend) GetReferenceStore ¶
func (b *InMemoryBackend) GetReferenceStore(id string) (*ReferenceStore, error)
GetReferenceStore retrieves a reference store by ID.
func (*InMemoryBackend) GetRun ¶
func (b *InMemoryBackend) GetRun(id string) (*Run, error)
GetRun retrieves a run, advancing PENDING→RUNNING→COMPLETED across polls (real RunRunningWaiter/RunCompletedWaiter clients poll GetRun until Status reaches RUNNING / COMPLETED respectively).
func (*InMemoryBackend) GetRunBatch ¶
func (b *InMemoryBackend) GetRunBatch(id string) (*RunBatch, error)
GetRunBatch retrieves a run batch.
func (*InMemoryBackend) GetRunBatchSummary ¶ added in v1.3.1
func (b *InMemoryBackend) GetRunBatchSummary(id string) (RunBatchSummary, error)
GetRunBatchSummary computes the live RunSummary breakdown for GetBatch's response.
func (*InMemoryBackend) GetRunCache ¶
func (b *InMemoryBackend) GetRunCache(id string) (*RunCache, error)
GetRunCache retrieves a run cache.
func (*InMemoryBackend) GetRunGroup ¶
func (b *InMemoryBackend) GetRunGroup(id string) (*RunGroup, error)
GetRunGroup retrieves a run group.
func (*InMemoryBackend) GetRunTask ¶
func (b *InMemoryBackend) GetRunTask(runID, taskID string) (*RunTask, error)
GetRunTask retrieves a task within a run, advancing PENDING→RUNNING→ COMPLETED across polls (real TaskRunningWaiter/TaskCompletedWaiter clients poll GetRunTask until Status reaches RUNNING / COMPLETED respectively).
func (*InMemoryBackend) GetS3AccessPolicy ¶
func (b *InMemoryBackend) GetS3AccessPolicy(s3AccessPointARN string) (*S3AccessPolicy, error)
GetS3AccessPolicy retrieves an S3 access policy.
func (*InMemoryBackend) GetSequenceStore ¶
func (b *InMemoryBackend) GetSequenceStore(id string) (*SequenceStore, error)
GetSequenceStore retrieves a sequence store by ID.
func (*InMemoryBackend) GetShare ¶
func (b *InMemoryBackend) GetShare(shareID string) (*Share, error)
GetShare retrieves a share, advancing ACTIVATING→ACTIVE on first poll, mirroring GetWorkflow/GetAnnotationStore/GetVariantStore's reap-on-read pattern. AcceptShare stamped Status ACTIVATING and nothing else in this backend ever advanced it -- a client polling GetShare for readiness never saw a terminal status. PENDING is left alone: it is the correct client-driven wait for AcceptShare/RejectShare, not a stall.
func (*InMemoryBackend) GetVariantImportJob ¶
func (b *InMemoryBackend) GetVariantImportJob(jobID string) (*VariantImportJob, error)
GetVariantImportJob retrieves a variant import job.
func (*InMemoryBackend) GetVariantStore ¶
func (b *InMemoryBackend) GetVariantStore(name string) (*VariantStore, error)
GetVariantStore retrieves a variant store, advancing CREATING→ACTIVE on first poll (real VariantStoreCreatedWaiter clients poll until Status == ACTIVE).
func (*InMemoryBackend) GetWorkflow ¶
func (b *InMemoryBackend) GetWorkflow(id string) (*Workflow, error)
GetWorkflow retrieves a workflow, advancing CREATING→ACTIVE on first poll (real WorkflowActiveWaiter clients poll GetWorkflow until Status == ACTIVE).
func (*InMemoryBackend) GetWorkflowVersion ¶
func (b *InMemoryBackend) GetWorkflowVersion( workflowID, versionName string, ) (*WorkflowVersion, error)
GetWorkflowVersion retrieves a workflow version, advancing CREATING→ACTIVE on first poll (real WorkflowVersionActiveWaiter clients poll until Status == ACTIVE).
func (*InMemoryBackend) ListAnnotationImportJobs ¶
func (b *InMemoryBackend) ListAnnotationImportJobs( filter *ImportJobFilter, ids0 []string, maxResults int, nextToken string, ) ([]*AnnotationImportJob, string, error)
ListAnnotationImportJobs lists annotation import jobs, optionally filtered by status/storeName and/or a specific set of job ids (real AWS ListAnnotationImportJobsInput body "filter"/"ids").
func (*InMemoryBackend) ListAnnotationStoreVersions ¶
func (b *InMemoryBackend) ListAnnotationStoreVersions( name string, filter *StoreStatusFilter, maxResults int, nextToken string, ) ([]*AnnotationStoreVersion, string, error)
ListAnnotationStoreVersions lists versions of an annotation store, optionally filtered by status (real AWS ListAnnotationStoreVersionsInput body "filter", omics@v1.49.5 serializers.go:5608).
func (*InMemoryBackend) ListAnnotationStores ¶
func (b *InMemoryBackend) ListAnnotationStores( filter *StoreStatusFilter, ids0 []string, maxResults int, nextToken string, ) ([]*AnnotationStore, string, error)
ListAnnotationStores lists annotation stores, optionally filtered by status and/or a specific set of store ids (real AWS ListAnnotationStoresInput body "filter"/"ids", omics@v1.49.5 serializers.go:5497).
func (*InMemoryBackend) ListConfigurations ¶
func (b *InMemoryBackend) ListConfigurations( maxResults int, nextToken string, ) ([]*Configuration, string, error)
ListConfigurations lists configurations.
func (*InMemoryBackend) ListMultipartReadSetUploads ¶
func (b *InMemoryBackend) ListMultipartReadSetUploads( sequenceStoreID string, maxResults int, nextToken string, ) ([]*MultipartReadSetUpload, string, error)
ListMultipartReadSetUploads lists in-progress multipart uploads.
func (*InMemoryBackend) ListReadSetActivationJobs ¶
func (b *InMemoryBackend) ListReadSetActivationJobs( sequenceStoreID string, maxResults int, nextToken string, ) ([]*ReadSetActivationJob, string, error)
ListReadSetActivationJobs lists read set activation jobs.
func (*InMemoryBackend) ListReadSetExportJobs ¶
func (b *InMemoryBackend) ListReadSetExportJobs( sequenceStoreID string, maxResults int, nextToken string, ) ([]*ReadSetExportJob, string, error)
ListReadSetExportJobs lists read set export jobs.
func (*InMemoryBackend) ListReadSetImportJobs ¶
func (b *InMemoryBackend) ListReadSetImportJobs( sequenceStoreID string, maxResults int, nextToken string, ) ([]*ReadSetImportJob, string, error)
ListReadSetImportJobs lists read set import jobs.
func (*InMemoryBackend) ListReadSetUploadParts ¶
func (b *InMemoryBackend) ListReadSetUploadParts( sequenceStoreID, uploadID string, maxResults int, nextToken string, ) ([]*ReadSetUploadPart, string, error)
ListReadSetUploadParts lists parts for a multipart read set upload.
func (*InMemoryBackend) ListReadSets ¶
func (b *InMemoryBackend) ListReadSets( sequenceStoreID string, filter *ReadSetFilter, maxResults int, nextToken string, ) ([]*ReadSetMetadata, string, error)
ListReadSets lists read sets in a sequence store.
func (*InMemoryBackend) ListReferenceImportJobs ¶
func (b *InMemoryBackend) ListReferenceImportJobs( referenceStoreID string, filter *ReferenceImportJobFilter, maxResults int, nextToken string, ) ([]*ReferenceImportJob, string, error)
ListReferenceImportJobs lists reference import jobs for a store, optionally filtered by status (real AWS ListReferenceImportJobsInput body "filter").
func (*InMemoryBackend) ListReferenceStores ¶
func (b *InMemoryBackend) ListReferenceStores( filter *ReferenceStoreFilter, maxResults int, nextToken string, ) ([]*ReferenceStore, string, error)
ListReferenceStores lists reference stores with optional name filter.
func (*InMemoryBackend) ListReferences ¶
func (b *InMemoryBackend) ListReferences( referenceStoreID string, filter *ReferenceFilter, maxResults int, nextToken string, ) ([]*ReferenceMetadata, string, error)
ListReferences lists references in a reference store.
func (*InMemoryBackend) ListRunBatches ¶
func (b *InMemoryBackend) ListRunBatches( filter *RunBatchFilter, maxResults int, nextToken string, ) ([]*RunBatch, string, error)
ListRunBatches lists run batches, optionally filtered by name/status (real AWS ListBatchInput query parameters). filter.RunGroupID is accepted for wire compatibility but not applied: real ListBatch filters by the run group of the batch's *contained runs*, and this simplified RunBatch model doesn't track a run-group association on the batch resource itself (see the PARITY.md RunBatch note on the broader BatchRunSettings/RunSummary gap).
func (*InMemoryBackend) ListRunCaches ¶
func (b *InMemoryBackend) ListRunCaches( maxResults int, nextToken string, ) ([]*RunCache, string, error)
ListRunCaches lists run caches.
func (*InMemoryBackend) ListRunGroups ¶
func (b *InMemoryBackend) ListRunGroups( filter *RunGroupFilter, maxResults int, nextToken string, ) ([]*RunGroup, string, error)
ListRunGroups lists run groups, optionally filtered by name (real AWS ListRunGroupsInput takes "name" as a query parameter).
func (*InMemoryBackend) ListRunTasks ¶
func (b *InMemoryBackend) ListRunTasks( runID string, filter *RunTaskFilter, maxResults int, nextToken string, ) ([]*RunTask, string, error)
ListRunTasks lists tasks within a run, optionally filtered by status (real AWS ListRunTasksInput "status" query parameter).
func (*InMemoryBackend) ListRuns ¶
func (b *InMemoryBackend) ListRuns(filter *RunFilter, maxResults int, nextToken string) ([]*Run, string, error)
ListRuns lists runs, optionally filtered by name/runGroupId/batchId/status (real AWS ListRunsInput query parameters).
func (*InMemoryBackend) ListRunsInBatch ¶
func (b *InMemoryBackend) ListRunsInBatch( batchID string, filter *RunsInBatchFilter, maxResults int, nextToken string, ) ([]*Run, string, error)
ListRunsInBatch lists runs that belong to a run batch, optionally filtered by runId and runSettingId (real AWS ListRunsInBatchInput query parameters). filter.SubmissionStatus is accepted for wire compatibility but not applied: this backend has no async submission-status state machine, since batches complete submission synchronously (see the PARITY.md RunBatch note).
func (*InMemoryBackend) ListSequenceStores ¶
func (b *InMemoryBackend) ListSequenceStores( filter *SequenceStoreFilter, maxResults int, nextToken string, ) ([]*SequenceStore, string, error)
ListSequenceStores lists sequence stores.
func (*InMemoryBackend) ListShares ¶
func (b *InMemoryBackend) ListShares( resourceOwner string, filter *ShareFilter, maxResults int, nextToken string, ) ([]*Share, string, error)
ListShares lists shares by resource owner, optionally filtered by resourceArns/status/type (real AWS ListSharesInput body "filter", omics@v1.49.5 types/types.go:678).
func (*InMemoryBackend) ListTagsForResource ¶
func (b *InMemoryBackend) ListTagsForResource(resourceARN string) (map[string]string, error)
ListTagsForResource returns all tags for a resource.
func (*InMemoryBackend) ListVariantImportJobs ¶
func (b *InMemoryBackend) ListVariantImportJobs( filter *ImportJobFilter, ids0 []string, maxResults int, nextToken string, ) ([]*VariantImportJob, string, error)
ListVariantImportJobs lists variant import jobs, optionally filtered by status/storeName and/or a specific set of job ids (real AWS ListVariantImportJobsInput body "filter"/"ids").
func (*InMemoryBackend) ListVariantStores ¶
func (b *InMemoryBackend) ListVariantStores( filter *StoreStatusFilter, ids0 []string, maxResults int, nextToken string, ) ([]*VariantStore, string, error)
ListVariantStores lists variant stores, optionally filtered by status and/or a specific set of store ids (real AWS ListVariantStoresInput body "filter"/"ids", omics@v1.49.5 serializers.go:7543).
func (*InMemoryBackend) ListWorkflowVersions ¶
func (b *InMemoryBackend) ListWorkflowVersions( workflowID string, filter *WorkflowVersionFilter, maxResults int, nextToken string, ) ([]*WorkflowVersion, string, error)
ListWorkflowVersions lists versions of a workflow, optionally filtered by type (real AWS ListWorkflowVersionsInput "type" query parameter).
func (*InMemoryBackend) ListWorkflows ¶
func (b *InMemoryBackend) ListWorkflows( filter *WorkflowFilter, maxResults int, nextToken string, ) ([]*Workflow, string, error)
ListWorkflows lists workflows, optionally filtered by name/type (real AWS ListWorkflowsInput query parameters).
func (*InMemoryBackend) PutS3AccessPolicy ¶
func (b *InMemoryBackend) PutS3AccessPolicy(s3AccessPointARN, policy string) error
PutS3AccessPolicy stores an S3 access policy.
func (*InMemoryBackend) Region ¶
func (b *InMemoryBackend) Region() string
Region returns the default region.
func (*InMemoryBackend) Restore ¶
func (b *InMemoryBackend) Restore(ctx context.Context, data []byte) error
Restore loads backend state from a JSON snapshot. It implements persistence.Persistable.
func (*InMemoryBackend) Snapshot ¶
func (b *InMemoryBackend) Snapshot(ctx context.Context) []byte
Snapshot serialises the backend state to JSON. It implements persistence.Persistable.
func (*InMemoryBackend) StartAnnotationImportJob ¶
func (b *InMemoryBackend) StartAnnotationImportJob( destinationName, roleARN string, items []AnnotationImportItem, annotationFields map[string]string, formatOptions map[string]any, runLeftNormalization bool, versionName string, ) (*AnnotationImportJob, error)
StartAnnotationImportJob starts an annotation import job. annotationFields, formatOptions, runLeftNormalization, and versionName are real optional StartAnnotationImportJobInput members (serializers.go:7892-7935) that were previously dropped on the floor -- the handler never read them at all.
func (*InMemoryBackend) StartReadSetActivationJob ¶
func (b *InMemoryBackend) StartReadSetActivationJob( sequenceStoreID string, sources []ReadSetActivationJobSource, ) (*ReadSetActivationJob, error)
StartReadSetActivationJob creates a read set activation job.
func (*InMemoryBackend) StartReadSetExportJob ¶
func (b *InMemoryBackend) StartReadSetExportJob( sequenceStoreID, destination string, sources []ReadSetExportJobSource, ) (*ReadSetExportJob, error)
StartReadSetExportJob creates a read set export job.
func (*InMemoryBackend) StartReadSetImportJob ¶
func (b *InMemoryBackend) StartReadSetImportJob( sequenceStoreID, roleARN string, sources []ReadSetImportJobSource, ) (*ReadSetImportJob, error)
StartReadSetImportJob creates a read set import job.
func (*InMemoryBackend) StartReferenceImportJob ¶
func (b *InMemoryBackend) StartReferenceImportJob( referenceStoreID, roleARN string, sources []ReferenceImportJobSource, ) (*ReferenceImportJob, error)
StartReferenceImportJob creates a reference import job.
func (*InMemoryBackend) StartRun ¶
func (b *InMemoryBackend) StartRun( workflowID, roleARN, name, runGroupID, runBatchID, networkingMode, runOutputURI string, params map[string]any, tags map[string]string, ) (*Run, error)
StartRun starts a new workflow run. networkingMode and runOutputURI are optional (real StartRunInput fields); runGroupID/runBatchID associate the run with a RunGroup/RunBatch for filtering via ListRuns.
func (*InMemoryBackend) StartRunBatch ¶
func (b *InMemoryBackend) StartRunBatch( batchName string, def DefaultRunSetting, inlineSettings []InlineRunSetting, tags map[string]string, ) (*RunBatch, error)
StartRunBatch starts a new run batch: it creates the RunBatch resource, then immediately creates one constituent Run per entry in inlineSettings (real BatchRunSettings.InlineSettings), merging each with def (real DefaultRunSetting) -- a run-level field is used when set, falling back to the batch default otherwise, matching the documented override semantics of types.InlineSetting. A duplicate RunSettingID within the same request is a submission failure for that entry (not a fatal error for the whole batch), matching real AWS's per-run submission-outcome model (see SubmissionSummary).
func (*InMemoryBackend) StartVariantImportJob ¶
func (b *InMemoryBackend) StartVariantImportJob( destinationName, roleARN string, items []VariantImportItem, annotationFields map[string]string, runLeftNormalization bool, ) (*VariantImportJob, error)
StartVariantImportJob starts a variant import job. annotationFields and runLeftNormalization are real optional StartVariantImportJobInput members (serializers.go:8737-8767) that were previously dropped on the floor -- the handler never read them at all. Unlike annotation import jobs, variant import jobs have no formatOptions or versionName field in the real API.
func (*InMemoryBackend) TagResource ¶
func (b *InMemoryBackend) TagResource(resourceARN string, tags map[string]string) error
TagResource adds tags to a resource identified by ARN.
func (*InMemoryBackend) UntagResource ¶
func (b *InMemoryBackend) UntagResource(resourceARN string, tagKeys []string) error
UntagResource removes tags from a resource identified by ARN.
func (*InMemoryBackend) UpdateAnnotationStore ¶
func (b *InMemoryBackend) UpdateAnnotationStore( name, description string, ) (*AnnotationStore, error)
UpdateAnnotationStore updates an annotation store.
func (*InMemoryBackend) UpdateAnnotationStoreVersion ¶
func (b *InMemoryBackend) UpdateAnnotationStoreVersion( name, versionName, description string, ) (*AnnotationStoreVersion, error)
UpdateAnnotationStoreVersion updates an annotation store version.
func (*InMemoryBackend) UpdateRunCache ¶
func (b *InMemoryBackend) UpdateRunCache(id, name, description string) error
UpdateRunCache updates a run cache.
func (*InMemoryBackend) UpdateRunGroup ¶
func (b *InMemoryBackend) UpdateRunGroup( id, name string, maxCPUs, maxRuns, maxDuration int, maxGPUs int, ) (*RunGroup, error)
UpdateRunGroup updates a run group.
func (*InMemoryBackend) UpdateSequenceStore ¶
func (b *InMemoryBackend) UpdateSequenceStore( id, name, description string, ) (*SequenceStore, error)
UpdateSequenceStore updates a sequence store's name and description.
func (*InMemoryBackend) UpdateVariantStore ¶
func (b *InMemoryBackend) UpdateVariantStore(name, description string) (*VariantStore, error)
UpdateVariantStore updates a variant store.
func (*InMemoryBackend) UpdateWorkflow ¶
func (b *InMemoryBackend) UpdateWorkflow(id, name, description string) error
UpdateWorkflow updates a workflow.
func (*InMemoryBackend) UpdateWorkflowVersion ¶
func (b *InMemoryBackend) UpdateWorkflowVersion(workflowID, versionName, description string) error
UpdateWorkflowVersion updates a workflow version.
func (*InMemoryBackend) UploadReadSetPart ¶
func (b *InMemoryBackend) UploadReadSetPart( sequenceStoreID, uploadID string, partNumber int, partSource string, data []byte, ) (string, error)
UploadReadSetPart stores binary data for a single part and returns its SHA256 checksum.
type InlineRunSetting ¶ added in v1.3.1
type InlineRunSetting struct {
RunTags map[string]string
Priority *int32
RunSettingID string
Name string
OutputURI string
}
InlineRunSetting is one caller-supplied per-run override within a StartRunBatch request's BatchRunSettings.InlineSettings list (real types.InlineSetting). Overrides Name/OutputURI/Priority/RunTags from DefaultRunSetting when set; RunSettingID is required and has no default.
type MultipartReadSetUpload ¶
type MultipartReadSetUpload struct {
CreationTime time.Time `json:"creationTime"`
Tags map[string]string `json:"tags"`
UploadID string `json:"uploadId"`
SequenceStoreID string `json:"sequenceStoreId"`
Name string `json:"name,omitempty"`
SourceFileType string `json:"sourceFileType"`
SampleID string `json:"sampleId"`
SubjectID string `json:"subjectId"`
// GeneratedFrom is real required MultipartReadSetUploadListItem's "generatedFrom"
// (List element, types.go) despite being optional on CreateMultipartReadSetUploadOutput
// -- present-but-empty (not omitted) is correct either way (gopherstack-r80d batch 7).
GeneratedFrom string `json:"generatedFrom"`
// ReferenceARN is real required CreateMultipartReadSetUploadOutput/
// MultipartReadSetUploadListItem "referenceArn" (api_op_CreateMultipartReadSetUpload.go:82-85,
// types.go) despite being an optional CreateMultipartReadSetUploadInput field --
// previously omitempty dropped the key entirely whenever a caller didn't supply
// one, which a real client decodes as a required-field-missing error
// (gopherstack-r80d batch 7).
ReferenceARN string `json:"referenceArn"`
Description string `json:"description,omitempty"`
}
MultipartReadSetUpload represents an in-progress multipart read set upload.
Field names/JSON keys were field-diffed against CreateMultipartReadSetUploadInput/Output and MultipartReadSetUploadListItem: the real wire key for the upload's file type is "sourceFileType" (this struct previously used the invented key "sequenceType", which appears nowhere in the real API), SampleID/SubjectID are real required fields that were previously missing entirely, and there is no real "status" field on this resource at all (removed).
type Provider ¶
type Provider struct{}
Provider implements service.Provider for AWS HealthOmics.
func (*Provider) Init ¶
func (p *Provider) Init(ctx *service.AppContext) (service.Registerable, error)
Init initializes the HealthOmics service backend and handler.
type ReadSetActivationJob ¶
type ReadSetActivationJob struct {
CreationTime time.Time `json:"creationTime"`
CompletionTime *time.Time `json:"completionTime,omitempty"`
ID string `json:"id"`
SequenceStoreID string `json:"sequenceStoreId"`
Status string `json:"status"`
Sources []ReadSetActivationJobSource `json:"sources"`
}
ReadSetActivationJob represents a read set activation job.
type ReadSetActivationJobSource ¶
type ReadSetActivationJobSource struct {
ReadSetID string `json:"readSetId"`
}
ReadSetActivationJobSource is a source for activating a read set.
type ReadSetBatchError ¶
type ReadSetBatchError struct {
ID string `json:"id"`
Code string `json:"code"`
Message string `json:"message"`
}
ReadSetBatchError is an error item from a batch delete operation.
type ReadSetExportJob ¶
type ReadSetExportJob struct {
CreationTime time.Time `json:"creationTime"`
CompletionTime *time.Time `json:"completionTime,omitempty"`
ID string `json:"id"`
SequenceStoreID string `json:"sequenceStoreId"`
Destination string `json:"destination"`
Status string `json:"status"`
Sources []ReadSetExportJobSource `json:"sources"`
}
ReadSetExportJob represents a read set export job.
type ReadSetExportJobSource ¶
type ReadSetExportJobSource struct {
ReadSetID string `json:"readSetId"`
}
ReadSetExportJobSource is a source for a read set export job.
type ReadSetFilter ¶
ReadSetFilter is filter criteria for listing read sets.
type ReadSetImportJob ¶
type ReadSetImportJob struct {
CreationTime time.Time `json:"creationTime"`
CompletionTime *time.Time `json:"completionTime,omitempty"`
ID string `json:"id"`
SequenceStoreID string `json:"sequenceStoreId"`
RoleARN string `json:"roleArn"`
Status string `json:"status"`
Sources []ReadSetImportJobSource `json:"sources"`
}
ReadSetImportJob represents a read set import job.
type ReadSetImportJobSource ¶
type ReadSetImportJobSource struct {
SourceFileType string `json:"sourceFileType"`
SourceFiles struct {
Source1 string `json:"source1"`
Source2 string `json:"source2,omitempty"`
} `json:"sourceFiles"`
SubjectID string `json:"subjectId"`
SampleID string `json:"sampleId"`
ReferenceARN string `json:"referenceArn"`
Name string `json:"name"`
Description string `json:"description"`
}
ReadSetImportJobSource is a source for a read set import job.
type ReadSetMetadata ¶
type ReadSetMetadata struct {
CreationTime time.Time `json:"creationTime"`
UpdateTime time.Time `json:"updateTime"`
Files map[string]any `json:"files,omitempty"`
Tags map[string]string `json:"tags"`
Arn string `json:"arn"`
ID string `json:"id"`
SequenceStoreID string `json:"sequenceStoreId"`
Name string `json:"name"`
Description string `json:"description"`
StatusMessage string `json:"statusMessage,omitempty"`
Status string `json:"status"`
// FileType is the real GetReadSetMetadataOutput/ReadSetListItem wire key
// ("fileType") -- confirmed against the SDK deserializer. It was
// previously (incorrectly) serialized as "sequenceType", a key that
// doesn't exist anywhere in the real API surface.
FileType string `json:"fileType"`
SubjectID string `json:"subjectId"`
SampleID string `json:"sampleId"`
ReferenceARN string `json:"referenceArn"`
}
ReadSetMetadata holds metadata for a read set.
type ReadSetUploadPart ¶
type ReadSetUploadPart struct {
LastUpdatedTime time.Time `json:"lastUpdatedTime"`
Checksum string `json:"checksum"`
Source string `json:"source"`
PartNumber int `json:"partNumber"`
PartSize int64 `json:"partSize"`
}
ReadSetUploadPart represents a single part of a multipart read set upload.
type ReferenceFilter ¶
type ReferenceFilter struct {
Name string
}
ReferenceFilter is filter criteria for listing references.
type ReferenceImportJob ¶
type ReferenceImportJob struct {
CreationTime time.Time `json:"creationTime"`
CompletionTime *time.Time `json:"completionTime,omitempty"`
ID string `json:"id"`
ReferenceStoreID string `json:"referenceStoreId"`
RoleARN string `json:"roleArn"`
Status string `json:"status"`
Sources []ReferenceImportJobSource `json:"sources"`
}
ReferenceImportJob represents a reference import job.
type ReferenceImportJobFilter ¶ added in v1.2.0
type ReferenceImportJobFilter struct {
Status string
}
ReferenceImportJobFilter is filter criteria for listing reference import jobs.
type ReferenceImportJobSource ¶
type ReferenceImportJobSource struct {
SourceFile string `json:"sourceFile"`
Name string `json:"name"`
Description string `json:"description"`
}
ReferenceImportJobSource is a source for a reference import job.
type ReferenceMetadata ¶
type ReferenceMetadata struct {
CreationTime time.Time `json:"creationTime"`
UpdateTime time.Time `json:"updateTime"`
Files map[string]any `json:"files,omitempty"`
Tags map[string]string `json:"tags"`
Arn string `json:"arn"`
ID string `json:"id"`
ReferenceStoreID string `json:"referenceStoreId"`
Name string `json:"name"`
Description string `json:"description"`
Status string `json:"status"`
MD5 string `json:"md5"`
}
ReferenceMetadata holds metadata for a genomic reference.
type ReferenceStore ¶
type ReferenceStore struct {
CreationTime time.Time `json:"creationTime"`
SseConfig map[string]any `json:"sseConfig,omitempty"`
S3Access map[string]any `json:"s3Access,omitempty"`
Tags map[string]string `json:"tags"`
Arn string `json:"arn"`
ID string `json:"id"`
Name string `json:"name"`
Description string `json:"description"`
}
ReferenceStore represents an HealthOmics reference store.
type ReferenceStoreFilter ¶
type ReferenceStoreFilter struct {
Name string
}
ReferenceStoreFilter is filter criteria for listing reference stores.
type Run ¶
type Run struct {
StartTime *time.Time `json:"startTime,omitempty"`
StopTime *time.Time `json:"stopTime,omitempty"`
CreationTime time.Time `json:"creationTime"`
Configuration *ConfigurationDetails `json:"configuration,omitempty"`
Tags map[string]string `json:"tags"`
Params map[string]any `json:"parameters"`
Arn string `json:"arn"`
ID string `json:"id"`
Name string `json:"name"`
WorkflowID string `json:"workflowId"`
RoleARN string `json:"roleArn"`
RunGroupID string `json:"runGroupId,omitempty"`
// RunBatchID is serialized as "batchId" (real GetRunOutput/RunListItem
// wire key -- confirmed against the SDK deserializer; there is no real
// StartRunInput field to set this, it's populated internally by
// DeleteRunsInBatch/ListRunsInBatch's caller association).
RunBatchID string `json:"batchId,omitempty"`
// RunSettingID mirrors the batch caller's InlineSetting.RunSettingId (real
// StartRunBatch request field, see types.InlineSetting) so ListRunsInBatch can map
// each created run back to the caller-supplied per-run configuration it came from.
// Empty for runs started via plain StartRun (there is no such field on that op).
RunSettingID string `json:"runSettingId,omitempty"`
NetworkingMode string `json:"networkingMode,omitempty"`
RunOutputURI string `json:"runOutputUri,omitempty"`
UUID string `json:"uuid,omitempty"`
Status string `json:"status"`
// contains filtered or unexported fields
}
Run represents an HealthOmics workflow run.
type RunBatch ¶
type RunBatch struct {
CreationTime time.Time `json:"creationTime"`
SubmittedTime time.Time `json:"submittedTime,omitzero"`
ProcessedTime time.Time `json:"processedTime,omitzero"`
Tags map[string]string `json:"tags"`
Arn string `json:"arn"`
ID string `json:"id"`
UUID string `json:"uuid"`
Name string `json:"name,omitempty"`
WorkflowID string `json:"workflowId"`
RoleARN string `json:"roleArn"`
RunGroupID string `json:"runGroupId,omitempty"`
OutputURI string `json:"outputUri,omitempty"`
Status string `json:"status"`
// TotalRuns is the number of constituent runs requested at submission time
// (len(InlineSettings)). SubmissionSuccessCount/SubmissionFailureCount and
// DeletedRunCount are one-time/monotonic outcomes of synchronous events
// (submission at StartRunBatch, deletion at DeleteRunsInBatch) and are stored
// directly rather than derived, since the Run rows they summarize either never
// existed (failed submissions) or are removed entirely (deleted runs) -- there is
// nothing left to recompute them from later. The remaining RunSummary counts
// (pending/running/completed/cancelled/failed) change as runs progress and are
// computed live from surviving Run rows by summarizeRunBatchLocked instead.
TotalRuns int32
SubmissionSuccessCount int32
SubmissionFailureCount int32
DeletedRunCount int32
}
RunBatch represents an HealthOmics run batch (real GetBatchOutput shape -- RunSummary/SubmissionSummary/TotalRuns are NOT stored here; they are computed live from the batch's constituent Run records by summarizeRunBatchLocked, since this backend creates/completes them synchronously and a stored, independently-updated counter would drift from the real Run rows it's meant to summarize).
type RunBatchFilter ¶ added in v1.2.0
RunBatchFilter is filter criteria for listing run batches (ListBatch).
type RunBatchSummary ¶ added in v1.3.1
type RunBatchSummary struct {
PendingRunCount int32
RunningRunCount int32
CompletedRunCount int32
CancelledRunCount int32
FailedRunCount int32
}
RunBatchSummary is the RunSummary breakdown (real types.RunSummary) computed live from a batch's surviving constituent Run rows.
type RunCache ¶
type RunCache struct {
CreationTime time.Time `json:"creationTime"`
Tags map[string]string `json:"tags"`
Arn string `json:"arn"`
ID string `json:"id"`
Name string `json:"name"`
Description string `json:"description,omitempty"`
CacheS3Location string `json:"cacheS3Uri"`
Status string `json:"status"`
}
RunCache represents an HealthOmics run cache.
type RunGroup ¶
type RunGroup struct {
CreationTime time.Time `json:"creationTime"`
Tags map[string]string `json:"tags"`
Arn string `json:"arn"`
ID string `json:"id"`
Name string `json:"name"`
MaxCPUs int `json:"maxCpus"`
MaxRuns int `json:"maxRuns"`
MaxDuration int `json:"maxDuration"`
MaxGPUs int `json:"maxGpus"`
}
RunGroup represents an HealthOmics run group.
type RunGroupFilter ¶ added in v1.2.0
type RunGroupFilter struct {
Name string
}
RunGroupFilter is filter criteria for listing run groups.
type RunTask ¶
type RunTask struct {
StartTime *time.Time `json:"startTime,omitempty"`
StopTime *time.Time `json:"stopTime,omitempty"`
CreationTime time.Time `json:"creationTime"`
TaskID string `json:"taskId"`
RunID string `json:"runId"`
Name string `json:"name"`
Status string `json:"status"`
CPUs int `json:"cpus"`
Memory int `json:"memory"`
// contains filtered or unexported fields
}
RunTask represents a task within a workflow run.
type RunTaskFilter ¶ added in v1.2.0
type RunTaskFilter struct {
Status string
}
RunTaskFilter is filter criteria for listing run tasks.
type RunsInBatchFilter ¶ added in v1.2.0
RunsInBatchFilter is filter criteria for listing the runs within a batch (ListRunsInBatch).
type S3AccessPolicy ¶
type S3AccessPolicy struct {
UpdateTime *time.Time `json:"updateTime,omitempty"`
S3AccessPointARN string `json:"s3AccessPointArn"`
Policy string `json:"s3AccessPolicy"`
StoreID string `json:"storeId,omitempty"`
StoreType string `json:"storeType,omitempty"`
}
S3AccessPolicy holds an S3 access policy for HealthOmics. S3AccessPolicy holds an S3 access policy for HealthOmics. Policy is serialized as "s3AccessPolicy" -- the real GetS3AccessPolicyOutput wire key (confirmed against the SDK deserializer); this struct previously used the key "policy", which real SDK clients never populate, so GetS3AccessPolicy responses were silently missing their policy document on the wire.
type SequenceStore ¶
type SequenceStore struct {
CreationTime time.Time `json:"creationTime"`
UpdateTime time.Time `json:"updateTime"`
SseConfig map[string]any `json:"sseConfig,omitempty"`
S3Access map[string]any `json:"s3Access,omitempty"`
Tags map[string]string `json:"tags"`
Arn string `json:"arn"`
ID string `json:"id"`
Name string `json:"name"`
Description string `json:"description"`
ETagAlgorithm string `json:"eTagAlgorithm,omitempty"`
Status string `json:"status"`
}
SequenceStore represents an HealthOmics sequence store.
type SequenceStoreFilter ¶
type SequenceStoreFilter struct {
Name string
}
SequenceStoreFilter is filter criteria for listing sequence stores.
type Share ¶
type Share struct {
// contains filtered or unexported fields
}
Share represents an HealthOmics resource share.
type ShareFilter ¶ added in v1.3.1
type ShareFilter struct {
}
ShareFilter is filter criteria for ListShares (real AWS types.Filter, omics@v1.49.5 types/types.go:678: resourceArns/status/type are each an "any of" list).
type StorageBackend ¶
type StorageBackend interface {
// ReferenceStore
CreateReferenceStore(name, description string, tags map[string]string) (*ReferenceStore, error)
DeleteReferenceStore(id string) error
GetReferenceStore(id string) (*ReferenceStore, error)
ListReferenceStores(
filter *ReferenceStoreFilter,
maxResults int,
nextToken string,
) ([]*ReferenceStore, string, error)
// Reference
DeleteReference(referenceStoreID, id string) error
GetReferenceMetadata(referenceStoreID, id string) (*ReferenceMetadata, error)
ListReferences(
referenceStoreID string,
filter *ReferenceFilter,
maxResults int,
nextToken string,
) ([]*ReferenceMetadata, string, error)
StartReferenceImportJob(
referenceStoreID, roleARN string,
sources []ReferenceImportJobSource,
) (*ReferenceImportJob, error)
GetReferenceImportJob(referenceStoreID, jobID string) (*ReferenceImportJob, error)
ListReferenceImportJobs(
referenceStoreID string,
filter *ReferenceImportJobFilter,
maxResults int,
nextToken string,
) ([]*ReferenceImportJob, string, error)
// SequenceStore
CreateSequenceStore(
name, description, eTagAlgorithmFamily, accessLogLocation string,
tags map[string]string,
) (*SequenceStore, error)
DeleteSequenceStore(id string) error
GetSequenceStore(id string) (*SequenceStore, error)
ListSequenceStores(
filter *SequenceStoreFilter,
maxResults int,
nextToken string,
) ([]*SequenceStore, string, error)
UpdateSequenceStore(id, name, description string) (*SequenceStore, error)
// ReadSet
BatchDeleteReadSet(sequenceStoreID string, ids []string) ([]ReadSetBatchError, error)
GetReadSetMetadata(sequenceStoreID, id string) (*ReadSetMetadata, error)
ListReadSets(
sequenceStoreID string,
filter *ReadSetFilter,
maxResults int,
nextToken string,
) ([]*ReadSetMetadata, string, error)
StartReadSetActivationJob(
sequenceStoreID string,
sources []ReadSetActivationJobSource,
) (*ReadSetActivationJob, error)
GetReadSetActivationJob(sequenceStoreID, jobID string) (*ReadSetActivationJob, error)
ListReadSetActivationJobs(
sequenceStoreID string,
maxResults int,
nextToken string,
) ([]*ReadSetActivationJob, string, error)
StartReadSetExportJob(
sequenceStoreID, destination string,
sources []ReadSetExportJobSource,
) (*ReadSetExportJob, error)
GetReadSetExportJob(sequenceStoreID, jobID string) (*ReadSetExportJob, error)
ListReadSetExportJobs(
sequenceStoreID string,
maxResults int,
nextToken string,
) ([]*ReadSetExportJob, string, error)
StartReadSetImportJob(
sequenceStoreID, roleARN string,
sources []ReadSetImportJobSource,
) (*ReadSetImportJob, error)
GetReadSetImportJob(sequenceStoreID, jobID string) (*ReadSetImportJob, error)
ListReadSetImportJobs(
sequenceStoreID string,
maxResults int,
nextToken string,
) ([]*ReadSetImportJob, string, error)
// Multipart ReadSet Upload
CreateMultipartReadSetUpload(
sequenceStoreID, name, sourceFileType, sampleID, subjectID, generatedFrom, referenceARN, description string,
tags map[string]string,
) (*MultipartReadSetUpload, error)
AbortMultipartReadSetUpload(sequenceStoreID, uploadID string) error
CompleteMultipartReadSetUpload(sequenceStoreID, uploadID string) (*ReadSetMetadata, error)
ListMultipartReadSetUploads(
sequenceStoreID string,
maxResults int,
nextToken string,
) ([]*MultipartReadSetUpload, string, error)
ListReadSetUploadParts(
sequenceStoreID, uploadID string,
maxResults int,
nextToken string,
) ([]*ReadSetUploadPart, string, error)
UploadReadSetPart(
sequenceStoreID, uploadID string,
partNumber int,
partSource string,
data []byte,
) (string, error)
GetReadSetBytes(sequenceStoreID, id string) ([]byte, error)
GetReferenceBytes(referenceStoreID, id string) ([]byte, error)
// RunGroup
CreateRunGroup(
name string,
maxCPUs, maxRuns, maxDuration int,
maxGPUs int,
tags map[string]string,
) (*RunGroup, error)
DeleteRunGroup(id string) error
GetRunGroup(id string) (*RunGroup, error)
ListRunGroups(filter *RunGroupFilter, maxResults int, nextToken string) ([]*RunGroup, string, error)
UpdateRunGroup(
id, name string,
maxCPUs, maxRuns, maxDuration int,
maxGPUs int,
) (*RunGroup, error)
// Run
StartRun(
workflowID, roleARN, name, runGroupID, runBatchID, networkingMode, runOutputURI string,
params map[string]any,
tags map[string]string,
) (*Run, error)
CancelRun(id string) error
DeleteRun(id string) error
GetRun(id string) (*Run, error)
ListRuns(filter *RunFilter, maxResults int, nextToken string) ([]*Run, string, error)
GetRunTask(runID, taskID string) (*RunTask, error)
ListRunTasks(
runID string,
filter *RunTaskFilter,
maxResults int,
nextToken string,
) ([]*RunTask, string, error)
// Workflow
CreateWorkflow(
name, description, definitionZip, definitionURI, engine string,
tags map[string]string,
) (*Workflow, error)
DeleteWorkflow(id string) error
GetWorkflow(id string) (*Workflow, error)
ListWorkflows(filter *WorkflowFilter, maxResults int, nextToken string) ([]*Workflow, string, error)
UpdateWorkflow(id, name, description string) error
// AnnotationStore
CreateAnnotationStore(
name, storeFormat string,
reference, sseConfig, storeOptions map[string]any,
tags map[string]string,
) (*AnnotationStore, error)
DeleteAnnotationStore(name string) (*AnnotationStore, error)
GetAnnotationStore(name string) (*AnnotationStore, error)
ListAnnotationStores(
filter *StoreStatusFilter,
ids []string,
maxResults int,
nextToken string,
) ([]*AnnotationStore, string, error)
UpdateAnnotationStore(name, description string) (*AnnotationStore, error)
StartAnnotationImportJob(
destinationName, roleARN string,
items []AnnotationImportItem,
annotationFields map[string]string,
formatOptions map[string]any,
runLeftNormalization bool,
versionName string,
) (*AnnotationImportJob, error)
GetAnnotationImportJob(jobID string) (*AnnotationImportJob, error)
ListAnnotationImportJobs(
filter *ImportJobFilter,
ids []string,
maxResults int,
nextToken string,
) ([]*AnnotationImportJob, string, error)
CancelAnnotationImportJob(jobID string) error
// AnnotationStoreVersion
CreateAnnotationStoreVersion(
name, versionName, description string,
tags map[string]string,
) (*AnnotationStoreVersion, error)
DeleteAnnotationStoreVersions(name string, versionNames []string) ([]VersionDeleteError, error)
GetAnnotationStoreVersion(name, versionName string) (*AnnotationStoreVersion, error)
ListAnnotationStoreVersions(
name string,
filter *StoreStatusFilter,
maxResults int,
nextToken string,
) ([]*AnnotationStoreVersion, string, error)
UpdateAnnotationStoreVersion(
name, versionName, description string,
) (*AnnotationStoreVersion, error)
// VariantStore
CreateVariantStore(name string, reference, sseConfig map[string]any, tags map[string]string) (*VariantStore, error)
DeleteVariantStore(name string) (*VariantStore, error)
GetVariantStore(name string) (*VariantStore, error)
ListVariantStores(
filter *StoreStatusFilter,
ids []string,
maxResults int,
nextToken string,
) ([]*VariantStore, string, error)
UpdateVariantStore(name, description string) (*VariantStore, error)
StartVariantImportJob(
destinationName, roleARN string,
items []VariantImportItem,
annotationFields map[string]string,
runLeftNormalization bool,
) (*VariantImportJob, error)
GetVariantImportJob(jobID string) (*VariantImportJob, error)
ListVariantImportJobs(
filter *ImportJobFilter,
ids []string,
maxResults int,
nextToken string,
) ([]*VariantImportJob, string, error)
CancelVariantImportJob(jobID string) error
// Share
resourceOwner string,
filter *ShareFilter,
maxResults int,
nextToken string,
) ([]*Share, string, error)
// RunCache
CreateRunCache(name, cacheS3Location string, tags map[string]string) (*RunCache, error)
DeleteRunCache(id string) error
GetRunCache(id string) (*RunCache, error)
ListRunCaches(maxResults int, nextToken string) ([]*RunCache, string, error)
UpdateRunCache(id, name, description string) error
// RunBatch
StartRunBatch(
batchName string, def DefaultRunSetting, inlineSettings []InlineRunSetting, tags map[string]string,
) (*RunBatch, error)
CancelRunBatch(id string) error
DeleteRunBatch(id string) error
GetRunBatch(id string) (*RunBatch, error)
GetRunBatchSummary(id string) (RunBatchSummary, error)
ListRunBatches(filter *RunBatchFilter, maxResults int, nextToken string) ([]*RunBatch, string, error)
DeleteRunsInBatch(batchID string) error
ListRunsInBatch(
batchID string,
filter *RunsInBatchFilter,
maxResults int,
nextToken string,
) ([]*Run, string, error)
// Configuration
CreateConfiguration(
name, description string, runConfigurations *ConfigurationRunConfigurations, tags map[string]string,
) (*Configuration, error)
DeleteConfiguration(name string) error
GetConfiguration(name string) (*Configuration, error)
ListConfigurations(maxResults int, nextToken string) ([]*Configuration, string, error)
// WorkflowVersion
CreateWorkflowVersion(
workflowID, versionName, description string,
tags map[string]string,
) (*WorkflowVersion, error)
DeleteWorkflowVersion(workflowID, versionName string) error
GetWorkflowVersion(workflowID, versionName string) (*WorkflowVersion, error)
ListWorkflowVersions(
workflowID string,
filter *WorkflowVersionFilter,
maxResults int,
nextToken string,
) ([]*WorkflowVersion, string, error)
UpdateWorkflowVersion(workflowID, versionName, description string) error
// S3 Access Policy
PutS3AccessPolicy(s3AccessPointARN, policy string) error
GetS3AccessPolicy(s3AccessPointARN string) (*S3AccessPolicy, error)
DeleteS3AccessPolicy(s3AccessPointARN string) error
// Tags
TagResource(resourceARN string, tags map[string]string) error
UntagResource(resourceARN string, tagKeys []string) error
ListTagsForResource(resourceARN string) (map[string]string, error)
AccountID() string
Region() string
Reset()
Snapshot(ctx context.Context) []byte
Restore(ctx context.Context, data []byte) error
}
StorageBackend is the interface for HealthOmics storage operations.
type StoreStatusFilter ¶ added in v1.3.1
type StoreStatusFilter struct {
Status string
}
StoreStatusFilter is filter criteria shared by ListAnnotationStores, ListVariantStores, and ListAnnotationStoreVersions (status only; real AWS ListAnnotationStoresFilter/ListVariantStoresFilter/ ListAnnotationStoreVersionsFilter, omics@v1.49.5 types/types.go:987,1018,997).
type VariantImportItem ¶
type VariantImportItem struct {
Source string `json:"source"`
}
VariantImportItem is a source item for a variant import job -- real types.VariantImportItemSource (types.go:2078-2086, omics@v1.49.5): Source only. This is StartVariantImportJobInput.Items' element shape, not the response shape GetVariantImportJobOutput.Items uses (see VariantImportItemDetail).
type VariantImportItemDetail ¶ added in v1.3.1
type VariantImportItemDetail struct {
JobStatus string `json:"jobStatus"`
Source string `json:"source"`
StatusMessage string `json:"statusMessage,omitempty"`
}
VariantImportItemDetail is the real GetVariantImportJobOutput.Items element, types.VariantImportItemDetail (types.go:2058-2071): JobStatus and Source are required, StatusMessage is optional. JobStatus is set once from the job's own Status at Start time (see variantImportItemDetails, variant_stores.go): this backend completes import jobs synchronously in one step, so every item reaches its final status in that same step. StatusMessage is always empty, same convention as the job-level StatusMessage below.
gopherstack-7s8r assumed ListVariantImportJobs also returns this shape; it does not -- the real List element (VariantImportJobItem, types.go:2090-2132) has no Items field at all. See VariantImportJobSummary.
type VariantImportJob ¶
type VariantImportJob struct {
CreationTime time.Time `json:"creationTime"`
CompletionTime *time.Time `json:"completionTime,omitempty"`
UpdateTime time.Time `json:"updateTime"`
AnnotationFields map[string]string `json:"annotationFields,omitempty"`
ID string `json:"id"`
DestinationName string `json:"destinationName"`
RoleARN string `json:"roleArn"`
Status string `json:"status"`
StatusMessage string `json:"statusMessage"`
Items []VariantImportItemDetail `json:"items"`
RunLeftNormalization bool `json:"runLeftNormalization,omitempty"`
}
VariantImportJob is the real GetVariantImportJobOutput shape (deserializers.go:11383-11444) and this backend's persisted job record.
ID is tagged "id" -- the real GetVariantImportJobOutput/ VariantImportJobItem wire key (deserializers.go:11383) -- which is right for Get/List but wrong for StartVariantImportJobOutput, whose only field is "jobId" (deserializers.go:18893); the start handler builds its own {"jobId": ...} response instead of marshaling this struct. ListVariantImportJobs doesn't marshal this struct either -- see VariantImportJobSummary. Unlike annotation import jobs, variant import jobs have no FormatOptions or VersionName field anywhere in the real API (StartVariantImportJobInput/GetVariantImportJobOutput both lack them) -- RunLeftNormalization/StatusMessage/UpdateTime are the real gaps here (deserializers.go:11406-11444), same schema-gap class as the annotation job. StatusMessage is always empty: this backend completes import jobs synchronously with no error state to describe.
type VariantImportJobSummary ¶ added in v1.3.1
type VariantImportJobSummary struct {
CreationTime time.Time `json:"creationTime"`
CompletionTime *time.Time `json:"completionTime,omitempty"`
UpdateTime time.Time `json:"updateTime"`
AnnotationFields map[string]string `json:"annotationFields,omitempty"`
ID string `json:"id"`
DestinationName string `json:"destinationName"`
RoleARN string `json:"roleArn"`
Status string `json:"status"`
RunLeftNormalization bool `json:"runLeftNormalization,omitempty"`
}
VariantImportJobSummary is the real ListVariantImportJobsOutput element, types.VariantImportJobItem (types.go:2090-2132). Deliberately narrower than VariantImportJob/GetVariantImportJobOutput: no Items or StatusMessage.
type VariantStore ¶
type VariantStore struct {
CreationTime time.Time `json:"creationTime"`
UpdateTime time.Time `json:"updateTime"`
Reference map[string]any `json:"reference,omitempty"`
// SseConfig is real GetVariantStoreOutput/VariantStoreItem's required
// "sseConfig" (types.go) -- previously not a field on this struct at
// all, the same "member with no struct field" class as
// AnnotationImportJob's pre-fix FormatOptions gap. CreateVariantStore
// now threads the real (optional) CreateVariantStoreInput.SseConfig
// through, mirroring AnnotationStore's existing convention
// (gopherstack-r80d batch 7).
SseConfig map[string]any `json:"sseConfig,omitempty"`
Tags map[string]string `json:"tags"`
StoreArn string `json:"storeArn"`
ID string `json:"id"`
Name string `json:"name"`
Description string `json:"description"`
Status string `json:"status"`
// StatusMessage is real GetVariantStoreOutput's required
// "statusMessage" -- previously absent from this struct entirely, the
// same gap fixed for import jobs in c41d36cb6 but missed here. Always
// empty: this backend transitions store status synchronously with no
// error state to describe.
StatusMessage string `json:"statusMessage"`
// StoreSizeBytes is real GetVariantStoreOutput's required
// "storeSizeBytes" (deserializers.go:11682). This backend does not track
// actual stored bytes -- always 0 rather than a fabricated number.
StoreSizeBytes int64 `json:"storeSizeBytes"`
// contains filtered or unexported fields
}
VariantStore represents an HealthOmics variant store.
StoreArn is real GetVariantStoreOutput/VariantStoreItem wire key "storeArn" (omics@v1.49.5 deserializers.go:11673) -- this struct previously tagged it "arn", a key no real Get/ListVariantStores deserializer reads.
type VariantStoreSummary ¶ added in v1.3.1
type VariantStoreSummary struct {
CreationTime time.Time `json:"creationTime"`
UpdateTime time.Time `json:"updateTime"`
Reference map[string]any `json:"reference,omitempty"`
SseConfig map[string]any `json:"sseConfig,omitempty"`
StoreArn string `json:"storeArn"`
ID string `json:"id"`
Name string `json:"name"`
Description string `json:"description"`
Status string `json:"status"`
StatusMessage string `json:"statusMessage"`
StoreSizeBytes int64 `json:"storeSizeBytes"`
}
VariantStoreSummary is the real ListVariantStoresOutput element shape (types.VariantStoreItem, omics@v1.49.5 types.go) -- narrower than GetVariantStoreOutput: no tags. ListVariantStores previously marshaled VariantStore directly, leaking it (gopherstack-dv4s).
SseConfig IS a real required VariantStoreItem member too (types.go), same as GetVariantStoreOutput -- fixed here alongside Get (gopherstack-r80d batch 7); this type's own doc comment previously called it "the opposite bug class from the one this pass targets", but it is exactly gopherstack-r80d's "member with no struct field at all" class.
type VersionDeleteError ¶
type VersionDeleteError struct {
VersionName string `json:"versionName"`
Code string `json:"code"`
Message string `json:"message"`
}
VersionDeleteError is an error item from a version delete operation.
type Workflow ¶
type Workflow struct {
CreationTime time.Time `json:"creationTime"`
Tags map[string]string `json:"tags"`
Arn string `json:"arn"`
ID string `json:"id"`
Name string `json:"name"`
Description string `json:"description"`
Engine string `json:"engine"`
Type string `json:"type,omitempty"`
UUID string `json:"uuid,omitempty"`
Status string `json:"status"`
// contains filtered or unexported fields
}
Workflow represents an HealthOmics workflow.
type WorkflowFilter ¶ added in v1.2.0
WorkflowFilter is filter criteria for listing workflows.
type WorkflowVersion ¶
type WorkflowVersion struct {
CreationTime time.Time `json:"creationTime"`
Tags map[string]string `json:"tags"`
Arn string `json:"arn"`
WorkflowID string `json:"workflowId"`
VersionName string `json:"versionName"`
Description string `json:"description"`
Engine string `json:"engine,omitempty"`
Type string `json:"type,omitempty"`
Status string `json:"status"`
// contains filtered or unexported fields
}
WorkflowVersion represents a version of a workflow.
type WorkflowVersionFilter ¶ added in v1.2.0
type WorkflowVersionFilter struct {
Type string
}
WorkflowVersionFilter is filter criteria for listing workflow versions.
Source Files
¶
- annotation_stores.go
- configurations.go
- handler.go
- handler_annotation_stores.go
- handler_configurations.go
- handler_read_sets.go
- handler_reference_stores.go
- handler_runs.go
- handler_sequence_stores.go
- handler_shares.go
- handler_tags.go
- handler_variant_stores.go
- handler_workflows.go
- interfaces.go
- models.go
- persistence.go
- provider.go
- read_sets.go
- reference_stores.go
- routes.go
- runs.go
- sequence_stores.go
- shares.go
- store.go
- store_setup.go
- tags.go
- variant_stores.go
- workflows.go