cli

type Attr struct {
	// Config commands
	Config *struct {
		ImportRclone *struct {
			Path string `arg:"positional" default:"~/.config/rclone/rclone.conf" help:"Path to existing rclone.conf to import"`
		} `arg:"subcommand:import-rclone" help:"Import an existing rclone.conf and print YAML fragment"`
	} `arg:"subcommand:config" help:"Configuration tools"`

	Server  string `arg:"-s,--server,env:SCITQ_SERVER" default:"localhost:50051" help:"gRPC server address"`
	TimeOut int    `arg:"-t,--timeout" default:"300" help:"Timeout for server interaction (in seconds)"`
	Token   string `arg:"-T,--token" default:"" help:"authentication token (used for tests)"`
	JSON    bool   `arg:"--json" help:"Output in JSON format (for scripting and AI agents)"`

	// Task Commands (Sub-Subcommands)
	Task *struct {
		Create *struct {
			Name         *string  `arg:"--name" help:"Optional name of the task"`
			Container    string   `arg:"--container,required" help:"Container to run"`
			Command      string   `arg:"--command,required" help:"Command to execute"`
			Shell        *string  `arg:"--shell" help:"Shell to use"`
			Input        []string `arg:"--input,separate" help:"Input values for the task (can be repeated)"`
			Resource     []string `arg:"--resource,separate" help:"Input values for the task (can be repeated)"`
			Output       string   `arg:"--output,separate" help:"Output folder where results are copied for the task"`
			StepId       *int32   `arg:"--step-id" help:"Step ID if task is affected to a step"`
			Dependencies []int32  `arg:"--dependency,separate" help:"IDs of tasks that this task depends on (can be repeated)"`
		} `arg:"subcommand:create" help:"Create a new task"`

		List *struct {
			Status     string `arg:"--status" help:"Filter tasks by status"`
			ShowHidden bool   `arg:"--show-hidden" help:"Include tasks marked as hidden (e.g., previous failed attempts)"`
			WorkerId   int32  `arg:"--worker-id" help:"Filter tasks by worker ID"`
			WorkflowId int32  `arg:"--workflow-id" help:"Filter tasks by workflow ID"`
			StepId     int32  `arg:"--step-id" help:"Filter tasks by step ID"`
			Command    string `arg:"--command" help:"Filter tasks by command substring"`
			Limit      int32  `arg:"--limit" default:"20" help:"Limit the number of tasks returned"`
			Offset     int32  `arg:"--offset" help:"Offset for pagination of tasks"`
			Long       bool   `arg:"-l,--long" help:"Show all task fields"`
		} `arg:"subcommand:list" help:"List all tasks"`

		Stdout *struct {
			ID int32 `arg:"--id,required" help:"Task ID"`
		} `arg:"subcommand:stdout" help:"Stream task stdout"`

		Stderr *struct {
			ID int32 `arg:"--id,required" help:"Task ID"`
		} `arg:"subcommand:stderr" help:"Stream task stderr"`

		Logs *struct {
			ID int32 `arg:"--id,required" help:"Task ID"`
		} `arg:"subcommand:logs" help:"Stream task stdout and stderr (colored)"`

		Retry *struct {
			ID    int32  `arg:"--id,required" help:"Task ID to retry"`
			Retry *int32 `arg:"--retry" help:"Number of retries left (optional)"`
		} `arg:"subcommand:retry" help:"Retry a failed task"`

		Edit *struct {
			ID      int32  `arg:"--id,required" help:"Task ID to edit and retry"`
			Command string `arg:"--command,required" help:"New command for the task"`
		} `arg:"subcommand:edit" help:"Edit a task's command and retry it"`

		Kill *struct {
			ID int32 `arg:"--id,required" help:"Task ID to kill"`
		} `arg:"subcommand:kill" help:"Send kill signal (SIGKILL) to a running task"`

		Stop *struct {
			ID    int32  `arg:"--id,required" help:"Task ID to stop"`
			Grace *int32 `arg:"--grace" help:"Grace period in seconds before SIGKILL (default: 10)"`
		} `arg:"subcommand:stop" help:"Send stop signal (SIGTERM) to a running task"`
	} `arg:"subcommand:task" help:"Manage tasks"`

	// Worker Commands (Sub-Subcommands)
	Worker *struct {
		List *struct {
			Long bool `arg:"-l,--long" help:"Show extended worker details"`
		} `arg:"subcommand:list" help:"List all workers"`
		Deploy *struct {
			Flavor      string `arg:"--flavor,required" help:"Worker flavor"`
			Provider    string `arg:"--provider,required" help:"Worker provider in the form providerName.configName like azure.primary"`
			Region      string `arg:"--region" help:"Worker region, default to provider default region"`
			Count       int    `arg:"--count" help:"How many worker to create" default:"1"`
			StepId      int32  `arg:"--step" help:"Worker step ID if worker is affected to a task"`
			Concurrency int    `arg:"--concurrency" default:"1" help:"Worker initial concurrency"`
			Prefetch    int    `arg:"--prefetch" default:"0" help:"Worker initial prefetch"`
		} `arg:"subcommand:deploy" help:"Create and deploy a new worker instance"`
		Delete *struct {
			WorkerId int32 `arg:"--worker-id,required" help:"The ID of the worker to be deleted"`
		} `arg:"subcommand:delete" help:"Delete a worker instance"`
		Update *struct {
			WorkerId        int32   `arg:"--worker-id,required" help:"The ID of the worker to update"`
			StepId          *int32  `arg:"--step-id" help:"Step ID to assign the worker to"`
			WorkflowName    *string `arg:"--workflow-name" help:"Workflow name to resolve step (lowest step_id if --step-name omitted)"`
			StepName        *string `arg:"--step-name" help:"Step name to resolve step (requires --workflow-name)"`
			Concurrency     *int32  `arg:"--concurrency" help:"Update worker concurrency"`
			Prefetch        *int32  `arg:"--prefetch" help:"Update worker prefetch"`
			Permanent       bool    `arg:"--permanent" help:"Set worker as permanent"`
			NoPermanent     bool    `arg:"--no-permanent" help:"Unset permanent status"`
			RecyclableScope *string `arg:"--recyclable-scope" help:"Update recyclable scope"`
		} `arg:"subcommand:update" help:"Update worker settings"`
		Stats *struct {
			WorkerIds []int32 `arg:"--worker-id,separate,required" help:"Worker IDs to get stats for"`
		} `arg:"subcommand:stats" help:"Fetch current stats for workers"`
	} `arg:"subcommand:worker" help:"Manage workers"`

	// Flavor commands
	Flavor *struct {
		List *struct {
			Limit  int    `arg:"--limit" help:"Limit the number of answers" default:"10"`
			Filter string `arg:"--filter" help:"Filter flavor by a filter string like 'cpu>=12:mem>=30'"`
		} `arg:"subcommand:list" help:"List flavors"`
	} `arg:"subcommand:flavor" help:"Find flavors"`

	// User commands
	User *struct {
		List   *struct{} `arg:"subcommand:list" help:"List all users"`
		Update *struct {
			UserId   int32   `arg:"--id,required" help:"User ID to update"`
			Username *string `arg:"--username" help:"New username"`
			Email    *string `arg:"--email" help:"New email"`
			Admin    bool    `arg:"--admin" help:"Set admin status"`
			NoAdmin  bool    `arg:"--no-admin" help:"Remove admin rights"`
		} `arg:"subcommand:update" help:"Update a user"`
		Create *struct {
			Username string `arg:"--username,required" help:"New username"`
			Email    string `arg:"--email,required" help:"New email"`
			Password string `arg:"--password,required" help:"New password"`
			Admin    bool   `arg:"--admin" help:"Set admin status"`
		} `arg:"subcommand:create" help:"Create a new user"`
		Delete *struct {
			UserId int32 `arg:"--id,required" help:"User ID to delete"`
		} `arg:"subcommand:delete" help:"Delete a user"`
		ChangePassword *struct {
			Username string `arg:"--username,required" help:"Username for which password will be changed"`
		} `arg:"subcommand:change-password" help:"Change your password"`
	} `arg:"subcommand:user" help:"User management"`

	Recruiter *struct {
		List *struct {
			StepId int32 `arg:"--step-id" help:"Step ID to filter"`
		} `arg:"subcommand:list" help:"List all recruiters"`
		Create *struct {
			StepId          int32    `arg:"--step-id,required" help:"Step ID"`
			Rank            int32    `arg:"--rank" default:"1" help:"Recruiter rank"`
			Protofilter     string   `arg:"--filter,required" help:"A filter like 'cpu>=12:mem>=30' or 'flavor~Standard_D2s_%:region is default'"`
			Concurrency     *int32   `arg:"--concurrency" help:"Worker initial concurrency"`
			Prefetch        *int32   `arg:"--prefetch" help:"Worker initial prefetch"`
			PrefetchPercent *int32   `arg:"--prefetch-percent" help:"Worker initial prefetc (expressed as a %% of concurrency)"`
			CpuPerTask      *int32   `arg:"--cpu-per-task" help:"Adaptative concurrency: CPU required for 1 task"`
			MemoryPerTask   *float32 `arg:"--memory-per-task" help:"Adaptative concurrency: Memory (Gb) required for 1 task"`
			DiskPerTask     *float32 `arg:"--disk-per-task" help:"Adaptative concurrency: Disk space (Gb) required for 1 task"`
			ConcurrencyMax  *int32   `arg:"--concurrency" help:"Adaptative concurrency: Maximum concurrency per worker"`
			ConcurrencyMin  *int32   `arg:"--concurrency" help:"Adaptative concurrency: Minimal concurrency per worker"`
			MaxWorkers      *int32   `arg:"--max-workers" help:"Maximum number of workers"`
			Rounds          int      `arg:"--rounds" help:"Number of rounds"`
			Timeout         int      `arg:"--timeout" default:"10" help:"Timeout in seconds"`
		} `arg:"subcommand:create" help:"Create a new recruiter"`
		Update *struct {
			StepId          int32    `arg:"--step-id,required" help:"Step ID"`
			Rank            int32    `arg:"--rank,required" help:"Recruiter rank"`
			Protofilter     *string  `arg:"--filter" help:"Updated filter (e.g. 'cpu>=12:mem>=30')"`
			Concurrency     *int32   `arg:"--concurrency" help:"Updated concurrency"`
			Prefetch        *int32   `arg:"--prefetch" help:"Updated prefetch"`
			PrefetchPercent *int32   `arg:"--prefetch-percent" help:"Updated prefetch (as %% of concurrency)"`
			CpuPerTask      *int32   `arg:"--cpu-per-task" help:"Updated CPU per task"`
			MemoryPerTask   *float32 `arg:"--memory-per-task" help:"Updated memory per task (GB)"`
			DiskPerTask     *float32 `arg:"--disk-per-task" help:"Updated disk per task (GB)"`
			ConcurrencyMax  *int32   `arg:"--concurrency-max" help:"Updated max concurrency"`
			ConcurrencyMin  *int32   `arg:"--concurrency-min" help:"Updated min concurrency"`
			MaxWorkers      *int32   `arg:"--max-workers" help:"Updated max workers"`
			Rounds          *int32   `arg:"--rounds" help:"Updated rounds"`
			Timeout         *int32   `arg:"--timeout" help:"Updated timeout (seconds)"`
		} `arg:"subcommand:update" help:"Update a recruiter"`
		Delete *struct {
			StepId int32 `arg:"--step-id,required" help:"Step ID to delete"`
			Rank   int   `arg:"--rank,required" help:"Recruiter rank to delete"`
		} `arg:"subcommand:delete" help:"Delete a recruiter"`
	} `arg:"subcommand:recruiter" help:"Recruiter management"`

	// Workflow commands
	Workflow *struct {
		List *struct {
			NameLike string `arg:"--name-like" help:"Filter workflows by name"`
		} `arg:"subcommand:list" help:"List workflows"`
		Create *struct {
			Name           string `arg:"--name,required" help:"Workflow name"`
			RunStrategy    string `` /* 283-byte string literal not displayed */
			MaximumWorkers *int32 `arg:"--maximum-workers" help:"Maximum number of workers"`
			Status         string `arg:"--status" help:"Initial workflow status (P/R/Z/D/F/S). Default is P."`
		} `arg:"subcommand:create" help:"Create a new workflow"`
		Update *struct {
			WorkflowId     int32  `arg:"--id,required" help:"Workflow ID to update"`
			Status         string `arg:"--status" help:"New workflow status (P/R/Z/D/F/S)"`
			MaximumWorkers *int32 `arg:"--maximum-workers" help:"Maximum number of workers"`
		} `arg:"subcommand:update" help:"Update a workflow"`
		Delete *struct {
			WorkflowId int32 `arg:"--id,required" help:"Workflow ID to delete"`
		} `arg:"subcommand:delete" help:"Delete a workflow"`
	} `arg:"subcommand:workflow" help:"Manage workflows"`

	// Step commands
	Step *struct {
		List *struct {
			WorkflowId int32 `arg:"--workflow-id,required" help:"Workflow ID to list steps for"`
		} `arg:"subcommand:list" help:"List steps for a workflow"`
		Create *struct {
			WorkflowId   int32  `arg:"--workflow-id" help:"Workflow ID"`
			WorkflowName string `arg:"--workflow-name" help:"Workflow name (alternative to ID)"`
			Name         string `arg:"--name,required" help:"Step name"`
		} `arg:"subcommand:create" help:"Create a step"`
		Delete *struct {
			StepId int32 `arg:"--id,required" help:"Step ID to delete"`
		} `arg:"subcommand:delete" help:"Delete a step"`
		Stats *struct {
			WorkflowId   *int32  `arg:"--workflow-id" help:"Workflow ID to get step stats for"`
			WorkflowName string  `arg:"--workflow-name" help:"Workflow name (alternative to ID, used to resolve ID)"`
			StepIds      []int32 `arg:"--step-id,separate" help:"Step IDs to get stats for (repeatable)"`
			TaskName     string  `arg:"--task-name" help:"Filter relevant step IDs by tasks whose name matches substring (case-insensitive, client-side)"`
			Totals       bool    `arg:"--totals" help:"Add totals line at the end of the stats"`
		} `arg:"subcommand:stats" help:"Show step statistics"`

		Edit *struct {
			StepId  int32  `arg:"--id,required" help:"Step ID"`
			Find    string `arg:"--find,required" help:"Text or regexp pattern to find in commands"`
			Replace string `arg:"--replace,required" help:"Replacement text"`
			Regexp  bool   `arg:"--regexp" help:"Treat --find as a regexp pattern"`
		} `arg:"subcommand:edit" help:"Find/replace in all failed tasks of a step and retry them"`
	} `arg:"subcommand:step" help:"Manage steps"`

	// File commands
	File *struct {
		RemoteList *struct {
			URI     string `arg:"positional,required" help:"URI to list files from (supports glob patterns)"`
			Timeout int    `arg:"--timeout" default:"30" help:"Timeout for listing files (in seconds)"`
		} `arg:"subcommand:remote-list" help:"List remote files"`
		Copy *struct {
			Src string `arg:"positional,required" help:"Source URI"`
			Dst string `arg:"positional,required" help:"Destination URI"`
		} `arg:"subcommand:copy" help:"Copy remote files"`

		List *struct {
			Src string `arg:"positional,required" help:"Source URI"`
		} `arg:"subcommand:list" help:"List remote files"`
	} `arg:"subcommand:file" help:"Remote file operations"`

	// (Workflow) Template commands
	Template *struct {
		Upload *struct {
			Path  string `arg:"--path,required" help:"Path to the Python template script"`
			Force bool   `arg:"--force" help:"Overwrite existing template with same name/version"`
		} `arg:"subcommand:upload" help:"Upload a new workflow template"`

		Run *struct {
			TemplateId   *int32  `arg:"--id" help:"ID of the template to run (either name or id is required)"`
			Name         *string `arg:"--name" help:"Name of the template to run (either name or id is required)"`
			Version      *string `arg:"--version" help:"Optional version (default to latest if omitted)"`
			ParamPairs   *string `arg:"--param" help:"Comma-separated key=value pairs (e.g. a=1,b=2)"`
			NoRecruiters bool    `arg:"--no-recruiters" help:"Create workflow without recruiters"`
		} `arg:"subcommand:run" help:"Run a workflow template"`

		List *struct {
			Name    *string `arg:"--name" help:"Template name (can include wildcards like 'meta%')"`
			Version *string `arg:"--version" help:"Template version (can be 'latest' or a wildcard)"`
			Latest  bool    `arg:"--latest" help:"Show only latest version(s) for each template name"`
		} `arg:"subcommand:list" help:"List all uploaded workflow templates"`

		Detail *struct {
			TemplateId *int32  `arg:"--id" help:"Show detailed information for this template ID (either name or id is required)"`
			Name       *string `arg:"--name" help:"Name of the template to show (either name or id is required)"`
			Version    *string `arg:"--version" help:"Optional version (default to latest if omitted)"`
		} `arg:"subcommand:detail" help:"Show a template's param JSON and metadata"`

		Download *struct {
			TemplateId *int32  `arg:"--id" help:"Template ID to download"`
			Name       *string `arg:"--name" help:"Name of the template to download"`
			Version    *string `arg:"--version" help:"Optional version (default to latest)"`
			Output     *string `arg:"--output,-o" help:"Output file path (default: stdout)"`
		} `arg:"subcommand:download" help:"Download a template script"`
	} `arg:"subcommand:template" help:"Manage workflow templates"`

	// Module commands
	Module *struct {
		Upload *struct {
			Path  string  `arg:"--path,required" help:"Path to the module YAML file"`
			As    *string `` /* 186-byte string literal not displayed */
			Force bool    `arg:"--force" help:"Overwrite an existing module at the same (path, version)"`
		} `arg:"subcommand:upload" help:"Upload a YAML module to the server's module library"`

		List *struct {
			Tree     bool    `arg:"--tree" help:"Group the list by folder (namespace tree view)"`
			Versions *string `arg:"--versions" help:"Show every version at this path (e.g. --versions genomics/fastp)"`
			Latest   bool    `arg:"--latest" help:"Show only the highest version per path"`
			Origin   *string `arg:"--origin" help:"Filter by origin: bundled, local or forked"`
		} `arg:"subcommand:list" help:"List modules in the server library"`

		Download *struct {
			Name   string  `arg:"--name,required" help:"Module reference (e.g. 'genetic/fastp' or 'genetic/fastp@1.2.0')"`
			Output *string `arg:"--output,-o" help:"Output file path (default: stdout)"`
		} `arg:"subcommand:download" help:"Download a module by name (optionally @version)"`

		Upgrade *struct {
			Apply bool `arg:"--apply" help:"Write changes to the DB (default: dry-run — only show the diff)"`
		} `arg:"subcommand:upgrade" help:"Seed/update bundled modules from the installed scitq2 package (admin-only)"`

		Origin *struct {
			Name string `arg:"positional,required" help:"Module reference (e.g. 'genetic/fastp' or 'genetic/fastp@1.2.0')"`
		} `arg:"subcommand:origin" help:"Show provenance of a module version (bundled / local / forked, content hash, uploader)"`

		Fork *struct {
			Source     string `arg:"positional,required" help:"Source reference (e.g. 'genetic/fastp@1.0.0'; bare name forks the latest)"`
			NewVersion string `arg:"--new-version,required" help:"Version of the forked row (e.g. '1.0.0-site')"`
		} `arg:"subcommand:fork" help:"Clone a module version into a new local fork (admin-only)"`
	} `arg:"subcommand:module" help:"Manage YAML modules (versioned library, bundled + local)"`

	// (Workflow) Template run commands
	Run *struct {
		List *struct {
			TemplateId *int32 `arg:"--template-id" help:"Filter runs by template ID"`
		} `arg:"subcommand:list" help:"List template runs"`

		Delete *struct {
			RunId int32 `arg:"--id,required" help:"ID of the template run to delete"`
		} `arg:"subcommand:delete" help:"Delete a template run"`
	} `arg:"subcommand:run" help:"Manage template runs"`

	// Login commands
	Login *struct {
		User     *string `arg:"--user" help:"Username to log in"`
		Password *string `arg:"--password" help:"Password to log in"`
	} `arg:"subcommand:login" help:"Login and provide a token, use with export SCITQ_TOKENs=$(scitq login)"`

	// Certificate command
	Cert *struct{} `arg:"subcommand:cert" help:"Print server TLS certificate (PEM)"`

	// HashPassword command
	HashPassword *struct {
		Password string `arg:"positional,required" help:"Password to hash"`
	} `arg:"subcommand:hashpassword" help:"Hash a password using bcrypt (useful for config files)"`

	// Worker event commands
	WorkerEvent *struct {
		List *struct {
			Limit    int    `arg:"--limit" default:"20" help:"Max number of events to show"`
			Level    string `arg:"--level" help:"Filter by level D/I/W/E as D:Debug/I:Info/W:Warning/E:Error"`
			Class    string `arg:"--class" help:"Filter by event_class"`
			WorkerId int32  `arg:"--worker-id" help:"Filter by worker id"`
		} `arg:"subcommand:list" help:"List worker events"`
		Delete *struct {
			Id int32 `arg:"--id,required" help:"Worker event ID to delete"`
		} `arg:"subcommand:delete" help:"Delete a worker event by ID"`
		Prune *struct {
			OlderThan string `arg:"--older-than" help:"Age to prune, e.g. 7d, 12h, 30m (required unless --dry-run)"`
			Level     string `arg:"--level" help:"Optional level filter D/I/W/E as D:Debug/I:Info/W:Warning/E:Error"`
			Class     string `arg:"--class" help:"Optional event_class filter"`
			WorkerId  int32  `arg:"--worker-id" help:"Optional worker id filter"`
			DryRun    bool   `arg:"--dry-run" help:"Only count matched rows; do not delete"`
		} `arg:"subcommand:prune" help:"Prune worker events by age and optional filters"`
	} `arg:"subcommand:worker-event" help:"Worker event logs"`
}

type CLI struct {
	QC   lib.QueueClient
	Attr Attr
}