cleve

type APIKey struct {
	Key     string
	User    string
	Created time.Time
}

type Analysis struct {
	AnalysisId string           `bson:"analysis_id" json:"analysis_id"`
	Path       string           `bson:"path" json:"path"`
	State      RunState         `bson:"state" json:"state"`
	Summary    *AnalysisSummary `bson:"summary" json:"summary"`
}

type AnalysisSummary struct {
	RunID           string `bson:"run_id" json:"run_id"`
	Result          string `bson:"result" json:"result"`
	SoftwareVersion string `bson:"software_version" json:"software_version"`
	Workflows       []struct {
		WorkflowName      string `bson:"workflow_name" json:"workflow_name"`
		ReportAggregation string `bson:"report_aggregation" json:"report_aggregation"`
		Samples           []struct {
			SampleID          string `bson:"sample_id" json:"sample_id"`
			BclToFastq        string `bson:"bcl_to_fastq" json:"bcl_to_fastq"`
			OraCompression    string `bson:"ora_compression" json:"ora_compression"`
			SecondaryAnalysis string `bson:"secondary_analysis" json:"secondary_analysis"`
			ReportGeneration  string `bson:"report_generation" json:"report_generation"`
		} `bson:"samples" json:"samples"`
	} `bson:"workflows" json:"workflows"`
}

type Gene struct {
	HGNC    int
	Symbol  string
	Aliases []string
}

type GenePanel struct {
	GenePanelVersion `bson:",inline" json:",inline"`
	Id               string    `json:"id"`
	Name             string    `json:"name"`
	Description      string    `json:"description"`
	Categories       []string  `json:"categories"`
	Genes            []Gene    `json:"genes,omitzero"`
	Archived         bool      `json:"archived"`
	ArchivedAt       time.Time `bson:",omitzero" json:"archived_at,omitzero"`
}

type GenePanelVersion struct {
	Version Version   `bson:"-" json:"version"`
	Date    time.Time `json:"date"`
}

type PaginationFilter struct {
	Page     int `form:"page,default=1"`
	PageSize int `form:"page_size"`
}

type PaginationMetadata struct {
	TotalCount int `bson:"total_count" json:"total_count"`
	Count      int `bson:"count" json:"count"`
	Page       int `bson:"page" json:"page"`
	PageSize   int `bson:"page_size" json:"page_size"`
	TotalPages int `bson:"total_pages" json:"total_pages"`
}

type PanelFilter struct {
	Category  string `form:"category"`
	Name      string `form:"name"`
	NameQuery string `form:"name_query"`
	Gene      string `form:"gene"`
	GeneQuery string `form:"gene_query"`
	HGNC      string `form:"hgnc"`
	Version   string `form:"version"`
	Archived  bool   `form:"archived"`
}

type Pipeline struct {
	Name    string `bson:"name" json:"name"`
	Version string `bson:"version" json:"version"`
	URL     string `bson:"url" json:"url"`
}

type Platform struct {
	Name          string
	InstrumentIds []string
	Aliases       []string
	ReadyMarker   string
	RunCount      int
}

type Platforms struct {
	Platforms []Platform
	// contains filtered or unexported fields
}

type QcFilter struct {
	RunId      string    `form:"run_id"`
	RunIdQuery string    `form:"run_id_query"`
	Platform   string    `form:"platform"`
	StartDate  time.Time `form:"start_time"`
	EndDate    time.Time `form:"end_time"`
	PaginationFilter
}

type QcResult struct {
	PaginationMetadata `bson:"metadata" json:"metadata"`
	InteropSummary     []interop.InteropSummary `bson:"interop" json:"interop"`
}

type Run struct {
	RunID            string                `bson:"run_id" json:"run_id"`
	ExperimentName   string                `bson:"experiment_name" json:"experiment_name"`
	Path             string                `bson:"path" json:"path"`
	Platform         string                `bson:"platform" json:"platform"`
	Created          time.Time             `bson:"created" json:"created"`
	StateHistory     []TimedRunState       `bson:"state_history" json:"state_history"`
	SampleSheet      *SampleSheetInfo      `bson:"samplesheet,omitempty" json:"samplesheet"`
	SampleSheetFiles []SampleSheetInfo     `bson:"samplesheets,omitempty" json:"samplesheets"`
	RunParameters    interop.RunParameters `bson:"run_parameters,omitzero" json:"run_parameters,omitzero"`
	RunInfo          interop.RunInfo       `bson:"run_info,omitzero" json:"run_info,omitzero"`
	Analysis         []*Analysis           `bson:"analysis,omitempty" json:"analysis,omitempty"`
	AnalysisCount    int                   `bson:"analysis_count" json:"analysis_count"`
}

type RunCompletionStatus struct {
	Status  string
	Message string
}

type RunFilter struct {
	RunID            string    `form:"run_id"`
	RunIdQuery       string    `form:"run_id_query"`
	Brief            bool      `form:"brief"`
	Platform         string    `form:"platform"`
	State            string    `form:"state"`
	From             time.Time `form:"from"`
	To               time.Time `form:"to"`
	PaginationFilter `form:",inline"`
}

type RunResult struct {
	PaginationMetadata `bson:"metadata" json:"metadata"`
	Runs               []*Run `bson:"runs" json:"runs"`
}

type RunState int

type RunningSummary[T uint32 | uint64 | float32 | float64] struct {
	Sum T

	Mean float64
	// contains filtered or unexported fields
}

type Sample struct {
	// Sample name. If missing it should be set to the sample ID.
	Name string `bson:"name" json:"name"`
	// Sample ID as listed in the samplesheet.
	Id string `bson:"id" json:"id"`
	// Paths to fastq files related to the sample.
	Fastq []string `bson:"fastq" json:"fastq"`
	// Analyses associated with the sample.
	Analyses []*SampleAnalysis `bson:"analyses" json:"analyses"`
}

type SampleAnalysis struct {
	Pipeline `bson:"pipeline" json:"pipeline"`
	Results  []SampleAnalysisResult `bson:"path" json:"path"`
}

type SampleAnalysisResult struct {
	Type        string   `bson:"type" json:"type"`
	Description string   `bson:"description" json:"description"`
	Path        []string `bson:"path" json:"path"`
}

type SampleFilter struct {
	Name             string `form:"sample_name"`
	Id               string `form:"sample_id"`
	RunId            string `form:"run_id"`
	Analysis         string `form:"analysis"`
	PaginationFilter `form:",inline"`
}

type SampleResult struct {
	PaginationMetadata `bson:"metadata" json:"metadata"`
	Samples            []Sample `bson:"samples" json:"samples"`
}

type SampleSheet struct {
	RunID    *string           `bson:"run_id" json:"run_id"`
	UUID     *uuid.UUID        `bson:"uuid" json:"uuid"`
	Files    []SampleSheetInfo `bson:"files" json:"files"`
	Sections []Section         `bson:"sections" json:"sections"`
}

type SampleSheetInfo struct {
	Path             string    `bson:"path" json:"path"`
	ModificationTime time.Time `bson:"modification_time" json:"modification_time"`
}

type Section struct {
	Name string      `bson:"name" json:"name"`
	Type SectionType `bson:"type" json:"type"`
	Rows [][]string  `bson:"rows" json:"rows"`
}

type SectionType int

type Time struct {
	time.Time
}

type TimedRunState struct {
	State RunState  `bson:"state" json:"state"`
	Time  time.Time `bson:"time" json:"time"`
}

type UpdateResult = mongo.UpdateResult

type Version struct {
	Major int
	Minor int
	Patch int
	// contains filtered or unexported fields
}