types

type BapiClisT struct {
	Quiet        bool
	HelpFlags    bool
	Version      string
	Proxy        string
	Retries      int
	Query        string
	Format       string
	Outfn        string
	Email        string
	Thread       int
	From         int
	Size         int
	RemoteName   bool
	Timeout      int
	RetSleepTime int
	CallCor      bool
}

type Datasets2toolsEndpoints struct {
	ObjectType              string
	PageSize                int
	DatasetAccession        string
	CannedAnalysisAccession string
	Query                   string
	ToolName                string
	DiseaseName             string
	Gneset                  string
}

type FmtClisT struct {
	Stdin       *[]byte
	Files       *[]string
	JSON        *map[int]map[string]interface{}
	Table       *map[int][]interface{}
	PrettyJSON  bool
	JSONToSlice bool
	JSONToCSV   bool
	Indent      int
	SortKeys    bool
}

type GdcAnnotations struct {
	Data struct {
		Hits []struct {
			AnnotationID          string      `json:"annotation_id"`
			CaseID                string      `json:"case_id"`
			CaseSubmitterID       string      `json:"case_submitter_id"`
			Category              string      `json:"category"`
			Classification        string      `json:"classification"`
			CreatedDatetime       string      `json:"created_datetime"`
			EntityID              string      `json:"entity_id"`
			EntitySubmitterID     string      `json:"entity_submitter_id"`
			EntityType            string      `json:"entity_type"`
			ID                    string      `json:"id"`
			LegacyCreatedDatetime string      `json:"legacy_created_datetime"`
			LegacyUpdatedDatetime interface{} `json:"legacy_updated_datetime"`
			Notes                 string      `json:"notes"`
			State                 string      `json:"state"`
			Status                string      `json:"status"`
			SubmitterID           string      `json:"submitter_id"`
			UpdatedDatetime       string      `json:"updated_datetime"`
		} `json:"hits"`
		Pagination struct {
			Count int    `json:"count"`
			From  int    `json:"from"`
			Page  int    `json:"page"`
			Pages int    `json:"pages"`
			Size  int    `json:"size"`
			Sort  string `json:"sort"`
			Total int    `json:"total"`
		} `json:"pagination"`
	} `json:"data"`
	Warnings struct{} `json:"warnings"`
}

type GdcCases struct {
	Data struct {
		Hits []struct {
			AliquotIds            []string    `json:"aliquot_ids"`
			CaseID                string      `json:"case_id"`
			CreatedDatetime       string      `json:"created_datetime"`
			DaysToLostToFollowup  interface{} `json:"days_to_lost_to_followup"`
			DiagnosisIds          []string    `json:"diagnosis_ids"`
			DiseaseType           string      `json:"disease_type"`
			ID                    string      `json:"id"`
			IndexDate             string      `json:"index_date"`
			LostToFollowup        interface{} `json:"lost_to_followup"`
			PrimarySite           string      `json:"primary_site"`
			SampleIds             []string    `json:"sample_ids"`
			State                 string      `json:"state"`
			SubmitterAliquotIds   []string    `json:"submitter_aliquot_ids"`
			SubmitterDiagnosisIds []string    `json:"submitter_diagnosis_ids"`
			SubmitterID           string      `json:"submitter_id"`
			SubmitterSampleIds    []string    `json:"submitter_sample_ids"`
			UpdatedDatetime       string      `json:"updated_datetime"`
		} `json:"hits"`
		Pagination struct {
			Count int    `json:"count"`
			From  int    `json:"from"`
			Page  int    `json:"page"`
			Pages int    `json:"pages"`
			Size  int    `json:"size"`
			Sort  string `json:"sort"`
			Total int    `json:"total"`
		} `json:"pagination"`
	} `json:"data"`
	Warnings struct{} `json:"warnings"`
}

type GdcEndpoints struct {
	Status      bool
	Projects    bool
	Cases       bool
	Files       bool
	Annotations bool
	Data        bool
	Manifest    bool
	Slicing     bool
	Legacy      bool
	ExtraParams GdcExtraParams
}

type GdcExtraParams struct {
	RemoteName bool
	Token      string
	Query      string
	Size       int
	From       int
	Sort       string
	Filter     string
	Pretty     bool
	JSON       bool
	Format     string
	Fields     string
	Expand     string
	Facets     string
}

type GdcFiles struct {
	Data struct {
		Hits []struct {
			Access          string      `json:"access"`
			Acl             []string    `json:"acl"`
			CreatedDatetime string      `json:"created_datetime"`
			DataCategory    string      `json:"data_category"`
			DataFormat      string      `json:"data_format"`
			DataRelease     string      `json:"data_release"`
			DataType        string      `json:"data_type"`
			ErrorType       interface{} `json:"error_type"`
			FileID          string      `json:"file_id"`
			FileName        string      `json:"file_name"`
			FileSize        int         `json:"file_size"`
			ID              string      `json:"id"`
			Md5sum          string      `json:"md5sum"`
			State           string      `json:"state"`
			StateComment    interface{} `json:"state_comment"`
			SubmitterID     string      `json:"submitter_id"`
			Type            string      `json:"type"`
			UpdatedDatetime string      `json:"updated_datetime"`
			Version         string      `json:"version"`
		} `json:"hits"`
		Pagination struct {
			Count int    `json:"count"`
			From  int    `json:"from"`
			Page  int    `json:"page"`
			Pages int    `json:"pages"`
			Size  int    `json:"size"`
			Sort  string `json:"sort"`
			Total int    `json:"total"`
		} `json:"pagination"`
	} `json:"data"`
	Warnings struct{} `json:"warnings"`
}

type GdcProjects struct {
	Data struct {
		Hits []struct {
			DbgapAccessionNumber string   `json:"dbgap_accession_number"`
			DiseaseType          []string `json:"disease_type"`
			ID                   string   `json:"id"`
			Name                 string   `json:"name"`
			PrimarySite          []string `json:"primary_site"`
			ProjectID            string   `json:"project_id"`
			Releasable           bool     `json:"releasable"`
			Released             bool     `json:"released"`
			State                string   `json:"state"`
		} `json:"hits"`
		Pagination struct {
			Count int    `json:"count"`
			From  int    `json:"from"`
			Page  int    `json:"page"`
			Pages int    `json:"pages"`
			Size  int    `json:"size"`
			Sort  string `json:"sort"`
			Total int    `json:"total"`
		} `json:"pagination"`
	} `json:"data"`
	Warnings struct{} `json:"warnings"`
}

type GdcStatus struct {
	Commit      string `json:"commit"`
	DataRelease string `json:"data_release"`
	Status      string `json:"status"`
	Tag         string `json:"tag"`
	Version     int    `json:"version"`
}

type NcbiClisT struct {
	NcbiDB        string
	NcbiRetmax    int
	NcbiXMLToJSON string
	NcbiXMLPaths  []string
	NcbiKeywords  string
}