types

type BapiClisT struct {
	TaskID       string
	Verbose      int
	SaveLog      bool
	LogDir       string
	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
	PrettyJSON   bool
	Indent       int
	SortKeys     bool
	Extra        string
	XML2json     bool
}

type BioToolsEndpoints struct {
	Tool         string
	ID           string
	Name         string
	Topic        string
	DataType     string
	DataFormat   string
	OutputFormat string
	Publication  string
}

type CligovEndpoints struct {
	InfoDataVrs       bool
	InfoAPIVrs        bool
	InfoAPIDefs       bool
	InfoStuStru       bool
	InfoStuFieldsList bool
	InfoStuStat       bool
	InfoSearchArea    bool
	FullStudies       bool
	StuFields         bool
	FieldValues       bool
	Field             string
	Fields            string
}

type Covid19Endpoints struct {
	AllRoute                        bool
	CountriesRoute                  bool
	CountryDayOneRoute              bool
	CountryDayOneTotalRoute         bool
	CountryRoute                    bool
	CountryStatusDayOneLiveRoute    bool
	CountryStatusDayOneRoute        bool
	CountryStatusDayOneTotalRoute   bool
	CountryStatusLiveRoute          bool
	CountryStatusRoute              bool
	CountryStatusTotalRoute         bool
	CountryTotalRoute               bool
	ExportRoute                     bool
	LiveCountryRoute                bool
	LiveCountryStatusAfterDateRoute bool
	LiveCountryStatusRoute          bool
	SummaryRoute                    bool
	WebhookRoute                    string

	Country string
	Status  string
	Date    string
}

type CrossRefDoiPost struct {
	Doi       string `json:"doi"`
	QueryType string `json:"queryType"`
	ResType   string `json:"resType"`
	DoiSearch string `json:"doi_search"`
}

type CrossRefEndpoints struct {
	Doi          CrossRefDoiPost
	ArticleTitle CrossRefTitlePost
	MetaData     CrossRefMetaPost
	SearchType   string `json:"search_type"`
	QueryType    string `json:"queryType"`
}

type CrossRefMetaPost struct {
	Auth        string `json:"auth"`
	ISSN        string `json:"issn"`
	Title       string `json:"title"`
	Atitle      string `json:"atitle"`
	Volume      string `json:"volume"`
	Issue       string `json:"issue"`
	Page        string `json:"page"`
	Year        string `json:"year"`
	ISBN        string `json:"isbn"`
	Compum      string `json:"compnum"`
	Stitle      string `json:"stitle"`
	ViewRecords string `json:"view_records"`
	SearchType  string `json:"search_type"`
	QueryType   string `json:"queryType"`
}

type CrossRefTitlePost struct {
	ArticleTitleSearch string `json:"article_title_search"`
	MultiHit           string `json:"multi_hit"`
	Atitle2            string `json:"atitle2"`
	Auth2              string `json:"auth2"`
	QueryType          string `json:"queryType"`
}

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

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 MgRastAnnoEndpoints struct {
	Evalue      int      `json:"evalue"`
	Filter      string   `json:"filter"`
	FilterLevel string   `json:"filter_level"`
	Format      string   `json:"format"`
	Identity    int      `json:"identity"`
	Length      int      `json:"length"`
	NoCutoffs   bool     `json:"no_cutoffs"`
	Source      string   `json:"source"`
	Type        string   `json:"type"`
	Version     int      `json:"version"`
	ID          string   `json:"id"`
	Md5s        []string `json:"md5s"`
}

type MgRastComputeEndpoints struct {
	Asynchronous bool        `json:"asynchronous"`
	Evalue       int         `json:"evalue"`
	Alpha        bool        `json:"alpha"`
	Rna          bool        `json:"rna"`
	Raw          int         `json:"raw"`
	AnnVer       int         `json:"ann_ver"`
	Level        string      `json:"level"`
	SeqNum       int         `json:"seq_num"`
	Md5          string      `json:"md5"`
	Columns      []string    `json:"columns"`
	Data         [][]float64 `json:"data"`
	Norm         string      `json:"norm"`
	Rows         []string    `json:"rows"`
	Distance     string      `json:"distance"`
	Cluster      string      `json:"cluster"`
	ID           string      `json:"id"`
	Retry        int         `json:"retry"`
}

type MgRastDownloadEndpoints struct {
	File   string `json:"file"`
	Link   bool   `json:"link"`
	AweID  string `json:"awe_id"`
	Delete bool   `json:"delete"`
	Force  bool   `json:"force"`
	Stage  string `json:"stage"`
}

type MgRastEndpoints struct {
	Info bool

	Annotation     bool   `json:"annotation"`
	Similarity     bool   `json:"similarity"`
	Sequence       string `json:"sequence"`
	Project        string
	ResearchObject string
	Library        string
	Sample         string

	ParamsAnno          MgRastAnnoEndpoints
	ParamsCompute       MgRastComputeEndpoints
	ParamsDownload      MgRastDownloadEndpoints
	ParamsProjOrLibrary MgRastProjLibEndpoints

	Compute               bool
	ComputeAlphadiversity bool
	ComputeRarefaction    bool
	ComputeBlast          bool
	ComputeNormalize      bool
	ComputeDistance       bool
	ComputeHeatmap        bool
	ComputePcoa           bool
	Rows                  string
	Data                  string
	Md5s                  string
	Columns               string
	ID                    string

	DarkMatter bool

	Download        bool
	DownloadHistory bool

	Inbox      bool
	M5nr       bool
	Matrix     bool
	MetaData   bool
	MetaGenome bool
	Mixs       bool
	Profile    bool
	Search     bool
	Submission bool
	Validation bool

	Auth string
}

type MgRastProjLibEndpoints struct {
	Limit     int    `json:"limit"`
	Offset    int    `json:"offset"`
	Order     string `json:"order"`
	Verbosity string `json:"Verbosity"`
}

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