Merge branch 'master' of github.com:friguzzi/swish into tutorial

.gitignore

@@ -1,5 +1,8 @@
+node_modules
 bower_components
+passwd
 storage
 log
+*.log
 *~
 *.swp

TODO.md

@@ -40,6 +40,9 @@
   - User provided rendering?
     - Allow for rewriting answer terms?
     - Allow generating HTML?  How to deal with security?
+  - Allow copy of Prolog representation.  See
+    http://www.javascriptkit.com/javatutors/copytoclipboard.shtml
+  - Allow download of rendered (HTML/SVG) representation.
 
 ## Sharing
 
@@ -71,6 +74,7 @@ _not_ see exactly the same UI for cooperation.  What about
     - etc ...
   - Make it easy to add HTTPS certificate based login.
     - not SWISH specific
+  - Change to digest login as default.
 
 ## Search
 

examples/exauc.pl

@@ -7,7 +7,10 @@
 
 main(AUCROC, ROC, AUCPR, PR):-
   compute_areas_diagrams(
-    [0.7 - a, 0.7 - a, 0.7 - \+(a), 0.6 - a, 0.6 - \+(a), 0.5 - a, 0.4 - \+(a)],
+    % list of couples prob-example where example is an atom for positive 
+    % examples and \+(atom) for negative examples
+    [0.7 - a, 0.7 - a, 0.7 - \+(a), 0.6 - a, 
+     0.6 - \+(a), 0.5 - a, 0.4 - \+(a)],
     AUCROC, ROC, AUCPR, PR).
 
 

examples/index.json

@@ -3,6 +3,7 @@
 [
 { "file":"inference_examples.swinb", "title":"cplint inference example programs"},
 { "file":"learning_examples.swinb", "title":"cplint learning example programs"},
+{ "file":"exauc.pl", "title":"AUC calculator"},
 { "file":"examples.swinb",	  "title":"Prolog Example programs" },
 "--",
 { "file":"dict.swinb",		  "title":"Dict tutorial" },

examples/inference_examples.swinb

@@ -29,6 +29,7 @@ This notebook gives an overview of example programs for inference.
   - Three sided dice ([threesideddice.cpl](example/threesideddice.cpl), 
   [threesideddice.pl](example/threesideddice.pl)  A three-sided die is repeatedly thrown until the outcome is three. From F. Riguzzi and T. Swift. _The PITA system: Tabling and answer subsumption for reasoning under uncertainty_. Theory and Practice of Logic Programming, 27th International Conference on Logic Programming (ICLP'11) Special Issue, 11(4-5), pages 433-449, 2011.
   - Mendelian inheritance of the color of pea plant - larger family ([mendelc.cpl](example/mendelc.cpl), [mendelc.pl](example/mendelc.pl)) From H. Blockeel. _Probabilistic logical models for mendel's experiments: An exercise_. In Inductive Logic Programming, Work in Progress Track, 2004.
+  - Meta probabilities ([meta.cpl](example/meta.cpl), [meta.pl](example/meta.pl)) Probabilities computation in the body of probabilistic clauses.
 </div>
 
 </div>

examples/meta.cpl

@@ -0,0 +1,20 @@
+/*
+Probabilities computation in the body of probabilistic clauses.
+*/
+
+a:0.2:-
+  prob(b,P),
+  P>0.2.
+
+b:0.5:-
+  c.
+
+c.
+
+:- end_cplint.
+
+/** <examples>
+
+?- a.
+
+*/

examples/meta.pl

@@ -0,0 +1,28 @@
+/*
+Probabilities computation in the body of probabilistic clauses.
+*/
+:- use_module(library(pita)).
+
+:- if(current_predicate(use_rendering/1)).
+:- use_rendering(c3).
+:- endif.
+
+:- cplint.
+
+a:0.2:-
+  prob(b,P),
+  P>0.2.
+
+b:0.5:-
+  c.
+
+c.
+
+:- end_cplint.
+
+/** <examples>
+
+?- prob(a,Prob).
+?- prob_bar(a,Prob).
+
+*/

lib/authenticate.pl

@@ -35,10 +35,23 @@
 :- use_module(library(debug)).
 :- use_module(library(crypt)).
 :- use_module(library(http/http_authenticate)).
+:- use_module(library(settings)).
 
 :- use_module(config).
 :- use_module(page).
 
+:- if(exists_source(library(http/http_digest))).
+:- use_module(library(http/http_digest)).
+:- setting(method, oneof([basic,digest]), digest,
+	   "HTTP authentication method used").
+:- else.
+:- setting(method, oneof([basic]), basic,
+	   "HTTP authentication method used").
+:- endif.
+
+:- setting(realm, atom, 'SWISH user',
+	   "HTTP authentication realm").
+
 :- multifile
 	swish_config:config/2,
 	swish_config:authenticate/2,
@@ -68,8 +81,14 @@
 	password_file_cache(File), !.
 password_file(File) :-
 	absolute_file_name(swish(passwd), File, [access(read)]),
+	update_auth_type(File),
 	asserta(password_file_cache(File)).
 
+logged_in(Request, User) :-
+	setting(method, digest), !,
+	setting(realm, Realm),
+	password_file(File),
+	http:authenticate(digest(File, Realm), Request, [user(User)|_Details]).
 logged_in(Request, User) :-
 	password_file(File),
 	http_authenticate(basic(File), Request, [User|_Fields]), !,
@@ -103,19 +122,59 @@
 	logged_in(Request, User).
 
 
+%%	update_auth_type(+File)
+%
+%	Update the authentication type to match the password hashes
+
+update_auth_type(File) :-
+	digest_password_file(File), !,
+	setting(method, Method),
+	(   Method == digest
+	->  true
+	;   print_message(warning, http_auth_type(Method, digest)),
+	    set_setting(method, digest)
+	).
+update_auth_type(_) :-
+	setting(method, Method),
+	(   Method == basic
+	->  true
+	;   print_message(warning, http_auth_type(Method, basic)),
+	    set_setting(method, basic)
+	).
+
+digest_password_file(File) :-
+	http_read_passwd_file(File, [passwd(_User, Hash, _Fields)|_]),
+	is_sha1(Hash).
+
+is_sha1(Hash) :-
+	atom_length(Hash, 32),
+	forall(sub_atom(Hash, _, 1, _, Char),
+	       char_type(Char, xdigit(_))).
+
 %%	swish_add_user(+User, +Passwd, +Fields) is det.
 %
 %	Add a new user to the SWISH password file.
 
+:- if(current_predicate(http_digest_password_hash/4)).
+swish_add_user(User, Passwd, Fields) :-
+	setting(method, digest), !,
+	setting(realm, Realm), !,
+	http_digest_password_hash(User, Realm, Passwd, Hash),
+	update_password(passwd(User, Hash, Fields)).
+:- endif.
 swish_add_user(User, Passwd, Fields) :-
 	phrase("$1$", E, _),		% use Unix MD5 hashes
 	crypt(Passwd, E),
 	string_codes(Hash, E),
+	update_password(passwd(User, Hash, Fields)).
 
-	Entry = passwd(User, Hash, Fields),
-
-	absolute_file_name(swish(passwd), File,
-			   [access(write)]),
+update_password(Entry) :-
+	arg(1, Entry, User),
+	(   catch(password_file(File), _, fail)
+	->  true
+	;   absolute_file_name(swish(passwd), File,
+			       [access(write)])
+	),
 	(   exists_file(File)
 	->  http_read_passwd_file(File, Data)
 	;   Data = []
@@ -126,3 +185,14 @@
 	),
 	http_write_passwd_file(File, NewData).
 
+
+		 /*******************************
+		 *	     MESSAGES		*
+		 *******************************/
+
+:- multifile prolog:message//1.
+
+prolog:message(http_auth_type(ReqMethod, Method)) -->
+	[ 'Using HTTP authentication ~q instead of ~q due to password file format'
+	  -[Method, ReqMethod]
+	].

lib/render/c3.pl

@@ -54,6 +54,10 @@
 %	Renders Term as a C3.js chart. This renderer recognises C3, as a
 %	dict with tag `c3`.
 
+% This renderer hooks into SWISH using two event-handlers and associated
+% classes. The `reactive-size` is called  after   the  window or pane is
+% resized and the `export-dom` is called from the _download_ button.
+
 term_rendering(C30, _Vars, _Options) -->
 	{ is_dict(C30, Tag),
 	  Tag == c3,
@@ -62,7 +66,7 @@
 	  atom_concat(#, Id, RefId),
 	  put_dict(bindto, C3, RefId, C3b)
 	},
-	html(div([ class(['render-C3', 'reactive-size']),
+	html(div([ class(['render-C3', 'reactive-size', 'export-dom']),
 		   'data-render'('As C3 chart')
 		 ],
 		 [ div(id(Id), []),
@@ -75,6 +79,17 @@
     var sizing = {};
     var tmo;
 
+    div.on("export-dom", function(ev, r) {
+      var svg = div.find("svg");
+      svg.attr("xmlns", "http://www.w3.org/2000/svg");
+      svg.css("font", "10px sans-serif");
+      svg.find(".c3-path,.c3-line,.tick,.domain").css("fill", "none");
+      svg.find(".tick,.domain").css("stroke", "#000");
+      r.element = svg[0];
+      r.extension = "svg";
+      r.contentType = "image/svg+xml";
+    });
+
     div.on("reactive-resize", function() {
       if ( chart ) {
 	if ( tmo ) clearTimeout(tmo);

lib/render/url.pl

@@ -0,0 +1,54 @@
+/*  Part of SWI-Prolog
+
+    Author:        Jan Wielemaker
+    E-mail:        [email protected]
+    WWW:           http://www.swi-prolog.org
+    Copyright (C): 2014, VU University Amsterdam
+
+    This program is free software; you can redistribute it and/or
+    modify it under the terms of the GNU General Public License
+    as published by the Free Software Foundation; either version 2
+    of the License, or (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public
+    License along with this library; if not, write to the Free Software
+    Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA
+
+    As a special exception, if you link this library with other files,
+    compiled with a Free Software compiler, to produce an executable, this
+    library does not by itself cause the resulting executable to be covered
+    by the GNU General Public License. This exception does not however
+    invalidate any other reasons why the executable file might be covered by
+    the GNU General Public License.
+*/
+
+:- module(swish_render_url,
+	  [ term_rendering//3			% +Term, +Vars, +Options
+	  ]).
+:- use_module(library(http/html_write)).
+:- use_module('../render').
+
+:- register_renderer(url, "Make URLs clickable").
+
+/** <module> SWISH url renderer
+
+Renders a URL as a clickable link
+*/
+
+%%	term_rendering(+URL, +Vars, +Options)//
+%
+%	Renders  a URL as a clickable link.
+
+term_rendering(URL, _Vars, _Options) -->
+	{   (   atom(URL)
+	    ->	true
+	    ;   string(URL)
+	    ),
+	    uri_is_global(URL)
+	},
+	html(a(href(URL), URL)).

swish.pl

@@ -175,10 +175,12 @@
 :- use_module(swish(lib/render/svgtree),  []).
 :- use_module(swish(lib/render/graphviz), []).
 :- use_module(swish(lib/render/c3),	  []).
+:- use_module(swish(lib/render/url),	  []).
 :- use_module(swish(lib/render/lpad),	  []).
 
 %:- use_module(lib/pita).
 :- use_module(library(pita)).
 :- use_module(library(slipcover)).
 :- use_module(library(auc)).
 
+

web/css/answer.css

@@ -15,7 +15,7 @@ div.render-multi {
 #render-select {
   position: absolute;
   background-color: #fff;
-  padding: 5px 20px;
+  padding: 5px 0px 5px 20px;
   border: 1px solid #000;
   border-radius: 5px;
   box-shadow: 5px 5px 5px #888;
@@ -34,6 +34,12 @@ div.render-multi {
   width: 20px; height: 20px;
 }
 
+div.render-item a {
+  float: right;
+  padding: 0px 10px 0px 10px;
+}
+
+
 		 /*******************************
 		 *	      ERRORS		*
 		 *******************************/

web/help/help-cplint.html

@@ -56,6 +56,11 @@ <h1 id="syn">Syntax</h1>
 <p>plus the predicate</p>
 <pre><code>average/2</code></pre>
 <p>that, given a list of numbers, computes its arithmetic mean.</p>
+<p>The body of rules may also contain the predicate <code>prob/2</code> that computes the probability of an atom, thus allowing nested probability computations. For example</p>
+<pre><code>a:0.2:-
+  prob(b,P),
+  P&gt;0.2.</code></pre>
+<p>is a valid rule.</p>
 <h1 id="inf">Inference</h1>
 <p><code>cplint</code> answers queries using the module <code>pita</code>. It performs the program transformation technique of <span class="citation">[7]</span>. Differently from that work, techniques alternative to tabling and answer subsumption are used.</p>
 <p>For answering queries, you have to prepare a Prolog file where you first load <code>pita</code> and then enclose the probabilistic clauses in <code>:-cplint.</code> and <code>:-end_cplint.</code> For example, the coin program above can be stored in <code>coin.pl</code> as follows</p>