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/repo.ml.html
Source file repo.ml
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open Lwt.Infix open Core open Bistro open Bistro_engine module W = Bistro_internals.Workflow type item = | Item : string list * _ path workflow -> item | Precious_item : _ path workflow -> item type t = item list type normalized_repo_item = { repo_path : string ; file_path : string ; cache_path : string ; } let normalized_repo_item ~repo_path ~id ~cache_path = { repo_path = Path.to_string repo_path ; file_path = Filename.concat "_files" id ; cache_path ; } let item path w = Item (path, w) let precious_item w = Precious_item w let ( %> ) path w = item path w let is_strict_prefix ~prefix u = String.length prefix < String.length u && String.is_prefix ~prefix u let find_bottom items item = let f min_item candidate = if is_strict_prefix ~prefix:candidate.cache_path min_item.cache_path then candidate else min_item in List.fold items ~init:item ~f (* FIXME: quadratic complexity *) let remove_redundancies repo = List.map repo ~f:(fun item -> let bottom = find_bottom repo item in if Poly.(bottom = item) then item else let cache_path = Filename.concat bottom.file_path (String.chop_prefix_exn ~prefix:bottom.cache_path item.cache_path) in { item with cache_path } ) let make_absolute p = if Filename.is_absolute p then p else Filename.concat (Sys.getcwd ()) p let make_relative ~from p = let open Path in make_relative ~from p |> to_string let link dst p_u = let target = make_absolute p_u in let dst_dir = Filename.dirname dst in let target_from_dst_dir = make_relative ~from:(make_absolute dst_dir) (make_absolute target) in Unix.mkdir_p dst_dir ; let cmd = sprintf "rm -rf '%s' && ln -s '%s' '%s'" dst target_from_dst_dir dst in ignore (Sys.command cmd) let generate outdir items = let items = remove_redundancies items in List.iter items ~f:(fun item -> let repo_path = Filename.concat outdir item.repo_path in let file_path = Filename.concat outdir item.file_path in let cache_path = if Filename.is_absolute item.cache_path then item.cache_path else Filename.concat outdir item.cache_path in link repo_path file_path ; link file_path cache_path ) let item_to_workflow = function | Item (repo_path, w) -> let%workflow id = W.id (Private.reveal w) in [normalized_repo_item ~repo_path ~id ~cache_path:[%path w]] | Precious_item _ -> Workflow.data [] let to_workflow ~outdir items = let normalized_items = List.map items ~f:item_to_workflow |> Workflow.list in [%workflow [%eval normalized_items] |> List.concat |> remove_redundancies |> generate outdir] let partition_results xs = let rec inner ok err = function | [] -> ok, err | Ok x :: t -> inner (x :: ok) err t | Error e :: t -> inner ok (e :: err) t in inner [] [] xs let protect sched items = List.iter items ~f:(function | Precious_item w -> Scheduler.protect sched w | Item _ -> () ) let build ?np ?mem ?loggers ?allowed_containers ?(bistro_dir = "_bistro") ?collect ~outdir repo = let db = Db.init_exn bistro_dir in let expressions = List.map repo ~f:(item_to_workflow) in let sched = Scheduler.create ?np ?mem ?loggers ?allowed_containers ?collect db in protect sched repo ; let results = Lwt_list.map_p (Scheduler.eval sched) expressions in Scheduler.start sched ; Lwt.map partition_results results >>= fun (res, errors) -> Scheduler.stop sched >|= fun () -> generate outdir (List.concat res) ; match errors with | [] -> () | _ :: _ -> ( let errors = List.concat errors |> Execution_trace.gather_failures in prerr_endline (Scheduler.error_report sched errors) ; failwith "Some workflow failed!" ) let build_main ?np ?mem ?loggers ?allowed_containers ?bistro_dir ?collect ~outdir repo = build ?np ?mem ?loggers ?allowed_containers ?bistro_dir ?collect ~outdir repo |> Lwt_main.run let add_prefix prefix items = List.map items ~f:(function | Item (p, w) -> Item (prefix @ p, w) | Precious_item _ as i -> i ) let shift dir items = add_prefix [ dir ] items let singleton dir w = [ [ dir ] %> w ] let protected_set repo = let rec fold_path_workflow acc (W.Any w) = match w with | Select s -> fold_path_workflow acc (W.Any s.dir) | Input _ -> acc | Shell _ | Plugin _ -> String.Set.add acc (W.id w) | Trywith tw -> fold_path_workflow (fold_path_workflow acc (W.Any tw.w)) (W.Any tw.failsafe) | Ifelse ie -> let acc = fold_path_workflow acc (W.Any ie.cond) in let acc = fold_path_workflow acc (W.Any ie._then_) in fold_path_workflow acc (W.Any ie._else_) | App _ | Both _ | Eval_path _ | Glob _ | List _ | List_nth _ | Pure _ | Spawn _ -> assert false in let k acc w = fold_path_workflow acc (W.Any (Bistro.Private.reveal w)) in List.fold repo ~init:String.Set.empty ~f:(fun acc it -> match it with | Item (_, w) -> k acc w | Precious_item w -> k acc w ) let cache_clip_fold ~bistro_dir repo ~f ~init = let protected = protected_set repo in let db = Db.init_exn bistro_dir in Db.fold_cache db ~init ~f:(fun acc id -> f db acc (if String.Set.mem protected id then `Protected id else `Unprotected id) ) let cache_clip_dry_run ~bistro_dir repo = cache_clip_fold ~bistro_dir repo ~init:(0,0,0,0) ~f:(fun db (total_files, total_size, deleted_files, deleted_size) item -> let id, protected = match item with | `Protected id -> id, true | `Unprotected id -> id, false in match Misc.du (Db.cache db id) with | Ok size -> let total_files = total_files + 1 in let total_size = total_size + size in if protected then (total_files, total_size, deleted_files, deleted_size) else (total_files, total_size, deleted_files + 1, deleted_size + size) | Error (`Msg msg) -> failwithf "du: %s" msg () ) let cache_clip ~bistro_dir repo = cache_clip_fold ~bistro_dir repo ~init:() ~f:(fun db () file -> match file with | `Protected _ -> () | `Unprotected id -> match Db.remove db id with | Ok () -> () | Error (`Msg msg) -> failwithf "cache_clip: %s" msg () )
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