package bistro

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package bistro

bistro
- Bistro
  - Private
  - Shell_dsl
  - Template_dsl
  - Workflow
  - binary_file
  - bz2
  - csv
  - directory_t
  - gz
  - html
  - pdf
  - png
  - regular_file_t
  - sexp_value
  - svg
  - tar
  - text
  - tsv
  - zip
bistro.engine
- Bistro_engine
  - Allocator
  - Db
  - Docker
  - Eval_thread
    
    Infix
  - Execution_env
  - Execution_trace
    
    Outcome
    
    Run_details
  - Local_backend
  - Logger
    
    t
  - Lwt_queue
  - Misc
  - Path
  - Scheduler
    
    Backend
    
    Gc
    
    Make
    
    Backend
  - Shell_command
  - Singularity
bistro.internals
- Bistro_internals
  - Command
  - Template
  - Workflow
    
    Any
    
    Map
    
    Set
    
    T
    
    Table
    
    Docker_image
    
    Singularity_image
bistro.multinode
- Bistro_multinode
  - Client
  - Server
bistro.nlp
- Bistro_nlp
  - Stanford_parser
    
    deps
bistro.script
- Bistro_script
bistro.unix
- Bistro_unix
  - Cmd
bistro.utils
- Bistro_utils
  - Console_logger
  - Dot_output
  - Html_logger
  - R_script
  - Repo
  - Report
    
    Md
  - Toplevel_eval
    
    Make
    
    P

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A database to cache workflow result and execution traces

It is implemented as a directory in the file system.

type t

An abstract type for databases

type id = string

val init : string -> (t, [ `Msg of string ]) Stdlib.result

init path creates a database located at path path, which can be absolute or relative. If the path already exists, its contents is inspected to see if it looks like a bistro database; if not, a fresh database is created on the filesystem.

Returns an error message if path is occupied with something else than a bistro database.

val init_exn : string -> t

raises Failure

val tmp_dir : t -> string

val cache_dir : t -> string

val stdout_dir : t -> string

val stderr_dir : t -> string

val build_dir : t -> string

val singularity_image_dir : t -> string

val tmp : t -> id -> string

val cache : t -> id -> string

val stdout : t -> id -> string

val stderr : t -> id -> string

val build : t -> id -> string

val singularity_image : 
  t ->
  Bistro_internals.Workflow.container_image ->
  string

val container_image_identifier : 
  Bistro_internals.Workflow.container_image ->
  string

val fold_cache : t -> init:'a -> f:('a -> id -> 'a) -> 'a

val path : t -> Bistro_internals.Workflow.path -> string

val is_in_cache : t -> Bistro_internals.Workflow.any -> bool

val remove : t -> id -> (unit, [> `Msg of string ]) Stdlib.result