package bistro
A library to build and run distributed scientific workflows
Install
Dune Dependency
Authors
Maintainers
Sources
bistro-0.6.0.tbz
sha256=146177faaaa9117a8e2bf0fd60cb658662c0aa992f35beb246e6fd0766050e66
sha512=553fe0c20f236316449b077a47e6e12626d193ba1916e9da233e5526dd39090e8677277e1c79baace3bdc940cb009f25431730a8efc00ae4ed9cc42a0add9609
doc/src/bistro.utils/html_logger.ml.html
Source file html_logger.ml
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open Core open Bistro_internals open Bistro_engine type time = float type event = | Step_workflow_started : { id : string ; descr : string ; } -> event | Workflow_ended : Execution_trace.Run_details.t -> event | Workflow_done_already : { w : _ Workflow.t ; path : string ; } -> event type model = { events : (time * event) list ; } let ( >>= ) = Lwt.( >>= ) let zone = Lazy.force Time.Zone.local type t = { path : string ; mutable model : model ; mutable changed : bool ; mutable stop : bool ; } let create path = { path ; model = { events = [] } ; stop = false ; changed = true ; } let translate_event db _ = function | Logger.Workflow_started (Shell {id ; descr ; _}, _) -> Some (Step_workflow_started { id ; descr }) | Workflow_ended { details ; _ } -> Some (Workflow_ended details) | Workflow_skipped (w, `Done_already) -> let path = Db.cache db (Workflow.id w) in Some (Workflow_done_already { w ; path }) | Workflow_ready _ | Workflow_allocation_error _ | Workflow_skipped (_, `Missing_dep) | Workflow_started (_, _) | Workflow_collected _ | Singularity_image_collected _ | Debug _ -> None let update model db time evt = { events = ( match translate_event db time evt with | None -> model.events | Some evt -> (time, evt) :: model.events ) ; } module Render = struct open Tyxml_html let new_elt_id = let c = ref 0 in fun () -> incr c ; sprintf "id%08d" !c let k = txt let kf fmt = Printf.ksprintf txt fmt let collapsible_panel ~title ~header ~body = let elt_id = new_elt_id () in [ div ~a:[a_class ["panel-group"]] [ div ~a:[a_class ["panel";"panel-default"]] [ div ~a:[a_class ["panel-heading"]] ( h4 ~a:[a_class ["panel-title"]] [ a ~a:[a_user_data "toggle" "collapse" ; a_href ("#" ^ elt_id) ] title ] :: header @ [ div ~a:[a_id elt_id ; a_class ["panel-collapse";"collapse"]] body ] ) ] ] ] let modal ~header ~body = let modal_id = new_elt_id () in let elt = div ~a:[a_id modal_id ; a_class ["modal";"fade"] ; Unsafe.string_attrib "role" "dialog"] [ div ~a:[a_class ["modal-dialog"] ; a_style "width:70%"] [ div ~a:[a_class ["modal-content"]] [ div ~a:[a_class ["modal-header"]] [ button ~a:[a_class ["close"] ; a_user_data "dismiss" "modal"] [ entity "times" ] ; h4 header ] ; div ~a:[a_class ["modal-body"]] body ] ] ] in modal_id, elt let item label contents = p (strong [k (label ^ ": ")] :: contents) let step_file_dumps = function | [] -> k"" ; | _ :: _ as dumps -> let modals = List.map dumps ~f:(fun (Shell_command.File_dump { text ; path }) -> let id, modal = modal ~header:[ k path ] ~body:[ pre [ k text ] ] in id, path, modal ) in let links = List.map modals ~f:(fun (modal_id, fn, _) -> li [ button ~a:[ a_class ["btn-link"] ; a_user_data "toggle" "modal" ; a_user_data "target" ("#" ^ modal_id)] [ k fn ] ] ) |> ul in div ( (item "file dumps" []) :: links :: List.map modals ~f:(fun (_,_,x) -> x) ) let shell_result_details ~id ~cmd ~cache ~stdout ~stderr ~file_dumps = let outputs = div [ item "outcome" [ a ~a:[a_href stdout ] [ k "stdout" ] ; k " " ; a ~a:[a_href stderr ] [ k "stderr" ] ; ] ; ] in [ item "id" [ match cache with | Some file_uri -> a ~a:[a_href file_uri] [ k id ] | None -> k id ] ; outputs ; div [ item "command" [] ; pre [ k cmd ] ; ] ; step_file_dumps file_dumps ; ] let task_result_header = function | `Succeeded -> k"" | `Error_exit_code i -> p [ kf "Command failed with code %d" i ] | `Plugin_failure msg -> p [ kf "Plugin failed with message: %s" msg ] | `Scheduler_error msg -> p [ kf "Scheduler error: %s" msg ] | `Missing_output -> p [ k "Missing output" ] let task_result = function | Execution_trace.Run_details.Input { path ; pass ; _ } -> [ p [ k "input " ; k path ] ; if pass then k"" else ( p [ k"Input doesn't exist" ] ) ] | Select { dir_path ; sel ; pass ; _ } -> [ p [ k "select " ; k (Bistro_engine.Path.to_string sel) ; k " in " ; k dir_path ] ; if pass then k"" else ( p [ k"No path " ; k (Bistro_engine.Path.to_string sel) ; k" in " ; a ~a:[a_href dir_path] [k dir_path ] ] ) ] | Shell { outcome ; stdout ; stderr ; cache ; file_dumps ; cmd ; descr ; id } -> collapsible_panel ~title:[ k descr ] ~header:[ task_result_header outcome ] ~body:(shell_result_details ~id:id ~cmd ~cache ~stderr ~stdout ~file_dumps) | Plugin res -> collapsible_panel ~title:[ k res.descr ] ~header:[ task_result_header res.outcome ] ~body:[] | Container_image_fetch f -> match f.outcome with | Ok () -> [ k"" ] | Error (`Singularity_failed_pull (_, url)) -> [ p [kf "Failed to fetch container image at %s" url] ] let workflow_start ~descr ~id = collapsible_panel ~title:[ k descr ] ~header:[] ~body:[ item "id" [ k id ] ; ] let cached_workflow : type s. s Workflow.t -> string -> _ = fun t path -> match t with | Workflow.Input { path ; _ } -> [ p [ k "input " ; k path ] ] | Select { dir = Input { path = input_path ; _ } ; sel ; _ } -> [ p [ k "select " ; k (Path.to_string sel) ; k " in " ; k input_path ] ] | Select { dir = Shell { id ; _ } ; sel ; _ } -> [ p [ k "select " ; k (Path.to_string sel) ; k " in step " ; k id ] ] | Select { dir = Select _ ; _} -> assert false | Shell { descr ; id ; _ } -> collapsible_panel ~title:[ k descr ] ~header:[] ~body:[ item "id" [ a ~a:[a_href path] [ k id ] ] ] | _ -> [] let event_label_text col text = let col = match col with | `BLACK -> "black" | `RED -> "red" | `GREEN -> "green" in let style = sprintf "color:%s; font-weight:bold;" col in span ~a:[a_style style] [ k text ] let result_label = function | Execution_trace.Run_details.Input { pass = true ; _ } | Select { pass = true ; _ } -> event_label_text `BLACK "CHECKED" | Input { pass = false ; _ } | Select { pass = false ; _ } | Plugin { outcome = (`Error_exit_code _ | `Plugin_failure _ | `Scheduler_error _) ; _ } | Shell { outcome = (`Error_exit_code _ | `Plugin_failure _ | `Scheduler_error _) ; _ } -> event_label_text `RED "FAILED" | Plugin { outcome = `Missing_output ; _ } | Shell { outcome = `Missing_output ; _ } -> event_label_text `RED "MISSING OUTPUT" | Shell { outcome = `Succeeded ; _ } | Plugin { outcome = `Succeeded ; _ } | Container_image_fetch { outcome = Ok () ; _ } -> event_label_text `GREEN "DONE" | Container_image_fetch { outcome = Error _ ; _ } -> event_label_text `RED "MISSING CONTAINER IMAGE" let event time evt = let table_line label details = [ td [ k Time.(to_string_trimmed ~zone (of_tm ~zone (Unix.localtime time))) ] ; td [ label ] ; td details ] in match evt with | Step_workflow_started { id ; descr } -> table_line (event_label_text `BLACK "STARTED") (workflow_start ~id ~descr) | Workflow_ended result -> table_line (result_label result) (task_result result) | Workflow_done_already { w ; path } -> table_line (event_label_text `BLACK "CACHED") (cached_workflow w path) let event_table m = let table = List.map m.events ~f:(fun (time, evt) -> tr (event time evt)) |> table ~a:[a_class ["table"]] in [ p ~a:[a_style {|font-weight:700; color:"#959595"|}] [ k"EVENT LOG" ] ; table ; ] let head = head (title (txt "Bistro report")) [ link ~rel:[`Stylesheet] ~href:"http://netdna.bootstrapcdn.com/bootstrap/3.0.2/css/bootstrap.min.css" () ; link ~rel:[`Stylesheet] ~href:"http://netdna.bootstrapcdn.com/bootstrap/3.0.2/css/bootstrap-theme.min.css" () ; script ~a:[a_src "https://code.jquery.com/jquery.js"] (txt "") ; script ~a:[a_src "http://netdna.bootstrapcdn.com/bootstrap/3.0.2/js/bootstrap.min.js"] (txt "") ; ] let model m = let contents = List.concat [ event_table m ; ] in html head (body [ div ~a:[a_class ["container"]] contents ]) end let save path doc = let buf = Buffer.create 253 in let formatter = Format.formatter_of_buffer buf in Tyxml_html.pp () formatter doc ; Lwt_io.with_file ~mode:Lwt_io.output path (fun oc -> let contents = Buffer.contents buf in Lwt_io.write oc contents ) let rec loop logger = if logger.changed then ( let doc = Render.model logger.model in logger.changed <- false ; save logger.path doc >>= fun () -> loop logger ) else if logger.stop then Lwt.return () else ( Lwt_unix.sleep 1. >>= fun () -> loop logger ) class logger path = let logger = create path in let loop = loop logger in object method event db time event = logger.model <- update logger.model db time event ; logger.changed <- true method stop = logger.stop <- true ; loop end let create path = new logger path
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