Skip to content

Commit

Permalink
shell
Browse files Browse the repository at this point in the history
  • Loading branch information
@cmungall
cmungall committed Nov 27, 2010
1 parent 1257abc commit de97591
Showing 1 changed file with 207 additions and 13 deletions.
220 changes: 207 additions & 13 deletions owl2_shell.pl
View file
Expand Up @@ -3,28 +3,39 @@
:- use_module(owl2_model).
:- use_module(owl2_plsyn).
:- use_module(owl2_util).
:- use_module(owl2_reasoner).
:- use_module(owl2_text_display).
:- use_module(owl2_popl,[popl_translate/1]).
:- use_module(owl2_dotty).

:- op(1100,xfy,--).
:- op(1090,fx,new).
:- op(1090,fx,add).
:- op(1090,fx,init).
:- op(1090,fx,rm).
:- op(1090,fx,m).
:- op(1090,fx,q).
:- op(1090,fx,rq).
:- op(1090,fx,v).
:- op(1090,fx,t).
:- op(1090,fx,l).
:- op(1090,fx,rq).
:- op(1090,fx,set).
:- op(1090,fx,unset).

:- op(1000,xfy,where).
:- op(800,xfy,to).
:- op(800,fx,(?)).

:- dynamic transaction/1.
:- dynamic redo_stack/1.

:- discontiguous cmd_doc/4.
:- multifile edit_template/2.

:- initialization(shell_init).

:- redefine_system_predicate('>'(_,_)).
:- redefine_system_predicate(help).

user:file_search_path(home, Home) :-
getenv('HOME',Home).
Expand All @@ -34,10 +45,18 @@
shell_init :-
set_prolog_flag(verbose,normal),
print_message(banner,thea_shell_welcome),
RDFS_Label='http://www.w3.org/2000/01/rdf-schema#label',
assert_axiom(annotationProperty(RDFS_Label)),
assert_axiom(annotationAssertion(RDFS_Label,RDFS_Label,literal(lang(en,label)))),
consult_rc.

consult_rc :-
rcfile(F),
exists_file(F),
!,
consult(F).
consult_rc.


save_settings :-
rcfile(F),
Expand All @@ -47,37 +66,199 @@
close(S).

% EDIT CMDS
edit_op(Op,AxiomIn) :- current_ontology(Ont),!,tr(AxiomIn,Axiom), Act =.. [Op,Axiom,Ont],Act,print_message(informational,Act),assertz(transaction(Act)).
cmd_doc(edit,new,[axiom],'Add axiom to current ontology').
cmd_doc(edit,add,[axiom],'Add axiom to current ontology').
cmd_doc(edit,rm,[axiom],'Retract axiom to current ontology').
cmd_doc(edit,undo,[],'Undo last add/rm').
cmd_doc(edit,redo,[],'Redo last undo').

edit_op(Op,AxiomIn) :- current_ontology(Ont),!,tr(AxiomIn,Axiom), Act =.. [Op,Axiom,Ont],Act,print_message(informational,Act),asserta(transaction(Act)).
edit_op(_,_) :- print_message(error,no_current_ontology).
add AxiomIn :- edit_op(assert_axiom,AxiomIn).
rm AxiomIn :- edit_op(retract_axiom,AxiomIn).
undo :- transaction(Act),undo(Act),print_message(informational,undo(Act)),assertz(redo_stack(Act)),retract(transaction(Act)).
undo :- transaction(Act),undo(Act),print_message(informational,undo(Act)),asserta(redo_stack(Act)),retract(transaction(Act)).
undo(assert_axiom(A,O)) :- retract_axiom(A,O).
undo(retract_axiom(A,O)) :- assert_axiom(A,O).
redo :- redo_stack(Act),Act,print_message(informational,redo(Act)),retract(redo_stack(Act)).
new Ont :- assert_axiom(ontology(Ont)),nb_setval(ontology,Ont).

% EDIT TEMPLATES
+(TN) :-
current_opts(Opts),
T=..[TN,IRI],
% example: template(X), [iri(prefix(obo)),class(X),N-annotationAssertion(label,X,N)]
edit_template(T,[iri(IRI_Template)|Fields]),
get_field_info(iri(IRI_Template),IRI),
%get_field_axiom_list(Fields,IRI,Axs_1),
findall(Ax,(member(Field,Fields),
get_field_axiom(Field,IRI,Ax)),
Axs_1),
flatten(Axs_1,Axs),
nl,
writeln('% ------------------'),
writeln('% AXIOMS TO ADD:'),
writeln('% ------------------'),
( member(display(combined),Opts)
-> Opts_2=Opts
; Opts_2=[display(combined)|Opts]),
forall(member(Ax,Axs),
( tr(Ax,Ax_2),
display_term(Ax_2,Opts_2))),
input('% OK? [enter for yes, any other char for no]',Ok),
nl,
( Ok=''
-> maplist(add,Axs),
writeln('% AXIOMS ADDED. Type "undo." to retract.')
; print_message(informational,not_added)).
/*
get_field_axiom_list([],_,[]).
get_field_axiom_list([Field|Fields],IRI,[Ax|Axs]) :-
get_field_axiom(Field,IRI,Ax),
get_field_axiom_list(Fields,IRI,Axs).
*/

get_field_info(iri(obo(Prefix)),IRI) :-
!,
get_field_info(iri(obo(Prefix,7)),IRI).
get_field_info(iri(obo(IDSpace,NumDigits)),IRI) :-
!,
concat_atom(['http://purl.obolibrary.org/obo/',IDSpace,'_'],Prefix),
get_field_info(iri(prefix(Prefix,NumDigits)),IRI).
get_field_info(iri(prefix(Prefix,NumDigits)),IRI) :-
findall(X,(entity(E),concat_atom([Prefix,X],E),is_numeric_atom(X)),Xs),
sort(Xs,SXs),
( reverse(SXs,[Last|_])
-> true
; Last='-1'),
atom_number(Last,LastID),
ID is LastID+1,
concat_atom(['~',NumDigits,'d'],Fmt),
format(atom(A1),Fmt,[ID]),sub_atom(A1,2,_,0,PaddedID),
atom_concat(Prefix,PaddedID,IRI).

get_field_axiom(multi(T),_,AxiomsOut) :-
!,
repeat,
( get_field_axiom(T,_,AxiomsOut)
-> true
; !,
fail).
get_field_axiom(Val-Axioms,_,AxiomsOut) :-
!,
repeat,
nl,
write('% Template: '),writeln(Axioms),
tr(Axioms,AxiomsOut),
write('% Enter value: '),write(Val),
input(' >> ',Val),
( Val=''
-> !,
fail
; \+ is_valid_axiom_list(AxiomsOut)
-> print_message(error,not_valid_axioms(AxiomsOut)),
fail
; format('% Val=~w~n',[Val]),
tr(AxiomsOut,AxiomsOut_2),
show(AxiomsOut_2),
!,
true).
get_field_axiom(Axiom,_,Axiom) :-
Axiom\=_-_,
Axiom\=multi(_),
!,
show(Axiom).
is_numeric_atom(A) :- catch(atom_number(A,_),_,fail).

input(Prompt,Val) :-
write(Prompt),
read_line_to_codes(user_input,Codes),
atom_codes(Val,Codes).

is_valid_axiom_list(L) :- is_list(L),!,forall(member(A,L),is_valid_axiom(A)).
is_valid_axiom_list(A) :- is_valid_axiom(A).


% DISPLAY CMDS
t N :- label2iri(N,X), current_opts(Opts), display_class_tree(X,Opts).
q QueryIn :- tr(QueryIn,Query), forall(Query,v(Query)).
cmd_doc(display,t,[class],'Show a tree').
cmd_doc(display,q,[term],'Query axioms').
cmd_doc(display,v,[axiom],'Query axioms').
cmd_doc(display,--,[cmd],'pipe through unix shell. E.g. q _<_ -- \'grep neuron\'.').

t N :- label2iri(N,X), nb_setval(obj,X),current_opts(Opts), display_class_tree(X,Opts).
l N :-
label2iri(N,X),
nb_setval(obj,X),
current_opts(Opts),
setof(A,
( axiom_references(A,X),
axiom_type(A,T)),
As),
format('* Axiom Type: ~w~n',[T]),
forall(member(A,As),
display_term(A,Opts)),
fail.
l _.

q SelectIn where QueryIn :- !,tr(QueryIn,Query),tr(SelectIn,Select), forall(Query,show(Select)).
q QueryIn :- !,tr(QueryIn,Query), forall(Query,show(Query)).
%q :- tr(Query,Axiom), q(_).
v Axiom :- current_opts(Opts),display_term(Axiom,Opts).
trshow(XIn) :- tr(XIn,X),show(X).
show(X) :- current_opts(Opts),display_term(X,Opts).
v ObjIn :- tr(ObjIn,Obj),current_opts(Opts),visualize_obj(Obj,Opts),read(_).
'--'(GoalIn,Cmd) :-
tr(GoalIn,Goal),
current_opts(Opts),
open(pipe(Cmd),write,S,[]),
forall(Goal,display_term(S,Goal,Opts)),
with_output_to(S,forall(Goal,true)),
close(S).
Cmd > File :- % TODO
open(File,write,S,[]),
with_output_to(S,Cmd),
close(S).

% LIST CMDS
cmd_doc(display,ls,[],'List ontologies').
cmd_doc(display,lsa,[],'List axioms in current ontology').

ls :-
forall(ontology(Ont),
( ( nb_current(ontology,Ont)
( ( current_ontology(Ont)
-> write('*')
; write(' ')),
writeln(Ont))).
lsa :-
current_ontology(Ont),
!,
current_opts(Opts),
forall(ontologyAxiom(Ont,A),
display_term(A,Opts)).
lsa :-
!,
current_opts(Opts),
forall(axiom(A),
display_term(A,Opts)).

cmd_doc(display,stats,[],'Stats on current ontology').
stats :- current_ontology(Ont),stats(Ont).
stats(Ont) :-
forall(aggregate(count,A,Arity^(ontologyAxiom(Ont,A),functor(A,T,Arity)),Num),
format('#~w\t~w~n',[T,Num])).

% REASONER CMDS
cmd_doc(reasoner,init,[name],'Initialize a reasoner on current ont. E.g. reasoner pellet.').
init RN :- initialize_reasoner(RN,_,[]).
rq SelectIn where QueryIn :- !,tr(QueryIn,Query),tr(SelectIn,Select), forall(reasoner_ask(Query),show(Select)).
rq QueryIn :- !,tr(QueryIn,Query), forall(reasoner_ask(Query),show(Query)).

rt(AxiomIn) :- tr(AxiomIn,Axiom),reasoner_ask(Axiom).
qt(AxiomIn) :- tr(AxiomIn,Axiom),Axiom.



% HELP
? X :- usage(X).
help :- usage.



set (P to V) :- !,unset(P), assert(settings(P,V)),save_settings.
set P + V :- !,assert(settings(P,V)),save_settings.
Expand All @@ -86,7 +267,8 @@
settings :- q(settings(_,_)).


tr(In,Out) :- plsyn_owl(In,Out),!.
%tr(In,Out) :- plsyn_owl(In,Out),!.
tr(In,Out) :- plsyn_owl(In,X),map_IRIs(get_IRI_from_label,X,Out).

:- multifile settings/2.
:- dynamic settings/2.
Expand All @@ -100,30 +282,42 @@
current_opts(Opts) :-
findall(Opt,
( settings(P,V),
atom(P),
Opt =.. [P,V]),
Opts).

current_ontology(Ont) :- nb_current(ontology,Ont),!.
current_ontology(Ont) :-
ontology(Ont),
!,
set_current_ontology(Ont).

set_current_ontology(Ont) :-
nb_setval(Ont),
nb_setval(ontology,Ont),
print_message(informational,shell('Set ontology to ~w'-[Ont])).

label2iri(Label,Obj) :- labelAnnotation_value(Obj,Label),!.
label2iri(X,X).


prolog:message(thea_shell_welcome) -->
['% ::: Welcome to Thea Shell :::'].
['% ::: Welcome to BOMB Shell :::'].

prolog:message(redo(Act)) --> ['Redo: '],prolog:message(Act).
prolog:message(undo(Act)) --> ['Undo: '],prolog:message(Act).
prolog:message(assert_axiom(A,Ont)) --> ['Asserting '],prolog:message(ax(A)),[' into ',Ont].
prolog:message(retract_axiom(A,Ont)) --> ['Retracting '],prolog:message(ax(A)),[' into ',Ont].
prolog:message(ax(Ax)) --> [Atom],{current_opts(Opts),with_output_to(atom(Atom),display_term(Ax,Opts))}.
prolog:message(shell(M)) --> [M].


usage :-
writeln('BOMB Shell Commands'),
forall(cmd_doc(_,C,_,Doc),
format('~w\t~w~n',[C,Doc])),
nl.
usage(C) :-
cmd_doc(_,C,_,Doc),
writeln(Doc).



0 comments on commit de97591

Please sign in to comment.