:- use_module(library(debug)).  %  simply to stop std_org/2 from complaining
:- use_module(library(options)).

% if library(lib) is missing, install via pack_install(lib).
%
:- use_module(library(lib) ).

% organism(mouse).

% stoics.org.uk packs, lib knowns how to deal with these (will install if missing)
:- lib(options).
% :- lib(debug_call).

% sets libs and download aliases
:- ensure_loaded(pack(bio_db/src/bio_db_build_aliases)).    % /1

% local libs
:- lib(std_org/2).

std_mouse_defaults(  [ debug(true),
                       iactive(true),
                       org(mouse)
                      ]
                  ).

/** std_mouse.

Build all the standard datasets for bio_db.

Dependencies
 * on([])
   maps_mgim,maps_ncbi,maps_reac,maps_unip
 * on(maps_mgim)
   maps_ense, maps_gont
 * on([maps_mgim,maps_unip])
   mouse_graphs_strg

Opts
  * debug(Dbg=true)
    progress, informational messages
  * iactive(Iact=true)
    whether the session is interactive, otherwise wget gets --no-verbose
  * org(Org=mouse)
    organism

@author nicos angelopoulos
@version  0.1 2017/10/12
@version  0.2 2018/03/30
@version  0.3 2018/11/05, everything tested, and working
@version  0.4 2020/09/11, added ense
@version  0.5 2022/12/27, added reac
@version  0.6 2025/09/26, added option(iactive(Iact))
@tbd add timings (in file)

*/
std_mouse( Args ) :-
    Self = std_mouse,
    options_append( Self, Args, Opts ),
    options( org(Org), Opts ),
    % bio_db_build_aliases( Opts ),
    % organism( Org ),
    std_org( Org, Opts ).

% not used. just makes human a valid debug token

std_mouse_debug( Org ) :-
    debug( mouse, 'finished all standards for: ~w', [Org] ).

std(mouse, maps, mgim).
std(mouse, maps, ense).
std(mouse, maps, ncbi).
std(mouse, maps, unip).
std(mouse, maps, gont).
std(mouse, maps, reac).

% std( mouse, graphs, gont ).
std(mouse, graphs, strg).