Merge branch 'master' of git+ssh://scm.gforge.inria.fr/gitroot/biocham/biocham

filename.pl

@@ -30,8 +30,10 @@ filename(Filename, ExpandedFilename) :-
     library_path(LibraryPath),
     Options = [relative_to(LibraryPath)]
   ;
-    Options = [],
-    SubFilename = Filename
+    SubFilename = Filename,
+    %Options = [], !bugwar: relative_to(Dir)!
+    working_directory(Dir, Dir),
+    Options = [relative_to(Dir)]
   ),
   absolute_file_name(SubFilename, ExpandedFilename, [expand(true) | Options]).
 

numerical_simulation.pl

@@ -173,6 +173,10 @@ convert_expression(- A, - AIndexed) :-
   !,
   convert_expression(A, AIndexed).
 
+convert_expression([A], - AIndexed) :-
+  !,
+  convert_expression(A, AIndexed).
+
 convert_expression(A + B, AIndexed + BIndexed) :-
   !,
   convert_expression(A, AIndexed),

nusmv.pl

@@ -219,5 +219,3 @@ reserved('EX').
 reserved('xor').
 
 reserved('R').
-
-

ode.pl

@@ -3,7 +3,8 @@
   [
     list_ODE/0,
     compute_ode/0,
-    ode/2
+    ode/2,
+    load_ode/1
   ]).
 
 :- dynamic(ode/2).
@@ -79,3 +80,40 @@ print_ode :-
       format('~f \td[~w]/dt=~w\n', [InitialConcentration, Molecule, Equation])
     )
   ).
+
+
+load_ode(InputFile) :-
+  biocham_command,
+  type(InputFile, input_file),
+  doc('
+    creates a new Biocham model (reaction rules, initial state, parameters and
+    macros) inferred from an xppaut .ode file (preferably written with
+    parameters).
+  '),
+  external_convert_ode(InputFile, 'external_ode.bc'),
+  load_biocham('external_ode.bc').
+
+
+add_ode(InputFile) :-
+  biocham_command,
+  type(InputFile, input_file),
+  doc('
+    adds reaction rules, initial state, parameters and
+    macros inferred from an xppaut .ode file (preferably written with
+    parameters).
+  '),
+  external_convert_ode(InputFile, 'external_ode.bc'),
+  add_biocham('external_ode.bc').
+
+
+external_convert_ode(InputFile, OutputFile) :-
+  setup_call_cleanup(
+    open('external_load_ode.bc', write, Ode_bc),
+    (
+      portray_clause(Ode_bc, load_ode(InputFile)),
+      portray_clause(Ode_bc, export_biocham(OutputFile)),
+      portray_clause(Ode_bc, 'quit')
+    ),
+    close(Ode_bc)
+  ),
+  call_subprocess(path(biocham), ['external_load_ode.bc'], [stdout(pipe(_))]).

ode.plt

@@ -13,4 +13,21 @@ test('compute_ode', [true(ODEs == [ode(b, a), ode(a, -a)])]) :-
     ODEs).
 
 
+test('load_ode', [true(Reactions = [[a] for a => b])]) :-
+  clear_model,
+  setup_call_cleanup(
+    open('test.ode', write, TestOde),
+    write(TestOde, '
+init a = 0
+init b = 0
+da/dt = -a
+db/dt = a
+done
+'),
+    close(TestOde)
+  ),
+  load_ode('test.ode'),
+  all_items([kind: reaction], Reactions).
+
+
 :- end_tests(ode).

plot.pl

@@ -64,8 +64,9 @@ export_plot(FileTemplate, Options) :-
   export_table(CsvFile),
   get_table_data([HeaderRow | _ ]),
   HeaderRow =.. [row, _TimeHeader | Headers],
+  absolute_file_name(PlotFile, AbsolutePlotFile),
   setup_call_cleanup(
-    open(PlotFile, write, Stream),
+    open(AbsolutePlotFile, write, Stream),
     export_plot_stream(Stream, CsvFile, Headers, Options),
     close(Stream)
   ).

reaction_rules.pl

@@ -117,6 +117,10 @@ kinetics((SimpleKinetics0, SimpleKinetics1)) :-
 :- grammar(simple_kinetics).
 
 
+simple_kinetics([A]) :-
+  simple_kinetics(A).
+
+
 simple_kinetics(SimpleKinetics0 + SimpleKinetics1) :-
   simple_kinetics(SimpleKinetics0),
   simple_kinetics(SimpleKinetics1).

tables.pl

@@ -74,7 +74,9 @@ export_table(OutputFile) :-
     TitleRow =.. [row | ColumnNames],
     Table = [TitleRow | Data]
   ),
-  csv_write_file(FilenameCsv, Table).
+  working_directory(Dir, Dir),
+  absolute_file_name(FilenameCsv, AbsoluteFilenameCsv, [relative_to(Dir)]),
+  csv_write_file(AbsoluteFilenameCsv, Table).
 
 
 list_tables :-

test.bc

-A <=> B.
-list_ODE.
-numerical_simulation.
-quit.
\ No newline at end of file
+% BIOCHAM model file
+
+% Reaction rules
+[a] for a=>b.
+
+% Initial state
+absent(a).
+absent(b).
+