Added hooks for firing messages when recipes are executed.

Default interceptor is a persistent store that logs actions
as unit clauses.

This could be extended to provide a complete workflow record,
as specified in #15

Author: cmungall

prolog/biomake/biomake.pl

@@ -117,6 +117,14 @@
 
 disable_backtrace :- assertz(no_backtrace).
 
+% ----------------------------------------
+% MESSAGE PASSING
+% ----------------------------------------
+
+:- multifile intercept_message_hook/1.
+fire_message(M) :-
+        findall(M,intercept_message_hook(M),_).
+
 
 % ----------------------------------------
 % TOP-LEVEL
@@ -175,7 +183,8 @@
 	dep_bindrule(Rule,Opts,Rule2,Opts2),  % test dependencies goal
         debug_report(build,'Post-dependency rule: ~w',[Rule2],SL),
         (   rebuild_required(T,DL,SL,Opts2)  % test if target is stale
-        ->  run_execs_and_update(Rule2,SL,Opts2)  % (re)build
+        ->  run_execs_and_update(Rule2,SL,Opts2),  % (re)build
+            fire_message(was_derived_from(T,DL,Rule2))
         ;   verbose_report('~w is up to date',[T],SL,Opts)),
 	!.
 build(T,SL,Opts) :-
@@ -458,6 +467,7 @@
         rule_dependencies(Rule,DL,Opts),
 	format(string(Cmd),"touch ~w",[T]),
 	shell(Cmd),
+        fire_message(was_generated_by(T,Cmd)),
 	(running_silent(T,Opts) -> true; report('~w',[Cmd],SL,Opts)),
 	update_hash(T,DL,Opts).
 dispatch_run_execs(Rule,SL,Opts) :-
@@ -545,6 +555,7 @@
         shell(Exec,Err),
         get_time(T2),
         DT is T2-T1,
+        fire_message(was_generated_by(T,Exec,Err,T1,T2)),
         debug_report(build,'  Return: ~w Time: ~w',[Err,DT],SL),
 	handle_exec_error(Exec,Err,T,SL,Opts),
         !.

prolog/biomake/cli.pl

@@ -310,6 +310,15 @@
 simple_arg('--one-shell',oneshell(true)).
 arg_info('--one-shell','','Run recipes in single shell (loosely equivalent to GNU Make\'s .ONESHELL)').
 
+% ----------------------------------------
+% PROVENANCE
+% ----------------------------------------
+
+parse_arg(['--dbpath',X|L],L,dbpath(X)).
+arg_info('--dbpath','PATH','Path db file for recording actions').
+simple_arg('--prov',prov(true)) :- ensure_loaded(library(biomake/persistent_db)).
+arg_info('--prov','','Provenance mode').
+
 % ----------------------------------------
 % MD5 CHECKSUMS
 % ----------------------------------------

prolog/biomake/persistent_db.pl

@@ -0,0 +1,42 @@
+:- module(persistent_db,
+          [
+           attach_persistent_db/1
+          ]).
+:- use_module(library(persistency)).
+
+:- persistent action(info:any, time:float, process_id:integer).
+
+:- dynamic attached/0.
+
+ensure_attached :-
+        attached,
+        !.
+ensure_attached :-
+        attach_persistent_db('.biomake-store.pro').
+
+ensure_exists(File) :-
+        exists_file(File),
+        !.
+ensure_exists(File) :-
+        tell(File),
+        told,
+        !.
+
+
+attach_persistent_db(File) :-
+        ensure_exists(File),
+        assert(attached),
+        db_attach(File, []).
+
+clear_persistent_db :-
+        with_mutex(persistent_db,
+                   retractall_action(_)).
+
+
+:- multifile biomake:intercept_message_hook/1.
+biomake:intercept_message_hook(M) :-
+        ensure_attached,
+        get_time(T),
+        current_prolog_flag(pid, PID),
+        assert_action(M,T,PID).
+