virgil/commit

ADD cooccurrence API

diff --git a/api/drugs.pl b/api/drugs.pl
index 29ccab3..616c1b8 100644
--- a/api/drugs.pl
+++ b/api/drugs.pl
@@ -1,5 +1,7 @@
 :- module(drugs,
-	  []).
+	  [drug_mention/4,
+	   drug_brand_name/3,
+	   drug_synonym/3]).
 
 :- use_module(library(http/http_dispatch)).
 :- use_module(library(http/http_parameters)).
@@ -31,18 +33,29 @@ http_drug_mentions(Request) :-
 
 drug_mentions(Q, Method, Mentions) :-
 	findall(Count-M,
-		(   setof(R, drug_mention(Method, Q, M, R), Rs),
+		(   setof(R, ( drug_mention(Method, Q, Lit, Use),
+			       rdf(R, aers:drug, Use),
+			       drug_normalise(Lit, M)
+			     ),
+			  Rs),
 		    length(Rs, Count)
 		),
 		Mentions0),
 	keysort(Mentions0, Mentions1),
 	reverse(Mentions1, Mentions).
 
-drug_mention(exact, Q, Normalised_Lit, Report) :-
-	rdf(DrugUse, aers:drugname, literal(exact(Q), Lit)),
-	rdf(Report, aers:drug, DrugUse),
-	drug_normalise(Lit, Normalised_Lit).
-drug_mention(Method, Q, Normalised_Lit, Report) :-
+drug_mention(exact, Q,  Lit, DrugUse) :-
+	!,
+	rdf(DrugUse, aers:drugname, literal(exact(Q), Lit)).
+drug_mention(brand, Q, Lit, DrugUse) :-
+	!,
+	drug_brand_name(drugbank, Q, Brand),
+	drug_mention(word, Brand, Lit, DrugUse).
+drug_mention(synonym, Q, Lit, DrugUse) :-
+	!,
+	drug_synonym(drugbank, Q, Synonym),
+	drug_mention(word, Synonym, Lit, DrugUse).
+drug_mention(Method, Q,	Lit, DrugUse) :-
 	(   Method = word
 	->  Query = case(Q)
 	;   Method = stem
@@ -59,9 +72,7 @@ drug_mention(Method, Q, Normalised_Lit, Report) :-
 	->  corrected_match(L, Lit, DrugUse)
 	;   rdf(DrugUse, aers:drugname, literal(L)),
 	    Lit = L
-	),
-	drug_normalise(Lit, Normalised_Lit),
-	rdf(Report, aers:drug, DrugUse).
+	).
 
 corrected_match(Name, Lit, DrugUse) :-
 	rdf(DrugUse, aers:drugname_corrected, literal(Name)),
diff --git a/api/reports.pl b/api/reports.pl
index 0ba40eb..85496bf 100644
--- a/api/reports.pl
+++ b/api/reports.pl
@@ -9,8 +9,10 @@
 :- use_module(library(semweb/rdf_describe)).
 :- use_module(library(semweb/rdf_json)).
 :- use_module(library(aers_report)).
+:- use_module(api(drugs)).
 
 :- http_handler(cliopatria(aers/api/reports), http_reports, []).
+:- http_handler(cliopatria(aers/api/cc), http_cc, []).
 
 
 %%	http_reports(+Request)
@@ -40,10 +42,94 @@ http_reports(Request) :-
 			 reaction=Reactions,
 			 reports=Reports_Limit])).
 
+http_cc(Request) :-
+	http_parameters(Request,
+			[drug(Drug,
+			      [atom,
+			       optional(true)
+			      ]),
+			 reaction(Reaction,
+				  [atom,
+				   optional(true)
+				  ]),
+			 drugMatch(DrugMatch0,
+				   [list(atom)
+				   ]),
+			 limit(Limit,
+			       [number,default(100)]),
+			 offset(Offset,
+				[number,default(0)])
+			]),
+	(   DrugMatch0 = []
+	->  DrugMatch = [word,brand,synonym,corrected]
+	;   DrugMatch = DrugMatch0
+	),
+	(   var(Drug),
+	    var(Reaction)
+	->  reply_json(json([error='api']))
+	;   (	Drug=all,
+	        Reaction=all
+	    ->  cc_count(Total),
+		CC = []
+	    ;   (nonvar(Drug),\+Drug==all)
+	    ->  drug_match(Drug, DrugMatch, DrugMentions),
+		drug_reaction_cc(DrugMentions, Reaction, CC),
+		length(CC, Total)
+	    ;   nonvar(Reaction)
+	    ->  drug_reaction_cc([], Reaction, CC),
+		length(CC, Total)
+	    ),
+	    list_offset(CC, Offset, CC_Offset),
+	    list_limit(CC_Offset, Limit, CC_Limit, _),
+	    maplist(cc_json, CC_Limit, CC_JSON),
+	    reply_json(json([totalNumberOfResults=Total,
+			     limit=Limit,
+			     offset=Offset,
+			     cc=CC_JSON]))
+	).
+
+drug_match(Drug, Methods, DrugMentions) :-
+	findall(M, ( member(Method, Methods),
+		     drug_mention(Method, Drug, M, _)
+		   ),
+		DrugMentions0),
+	sort(DrugMentions0, DrugMentions).
+
+drug_reaction_cc([], ReactionMention, []) :-
+	(var(ReactionMention); ReactionMention==all),
+	!.
+drug_reaction_cc([], ReactionMention, CC) :-
+	nonvar(ReactionMention),
+	!,
+	findall(cc(Report,Drug,Reaction),
+	      (	  rdf(Report, aers:reaction, literal(exact(ReactionMention), Reaction)),
+		  rdf(Report, aers:drug, DrugUse),
+		  rdf(DrugUse, aers:drugname, literal(Drug))
+	      ),
+	      CC0),
+	sort(CC0, CC).
+drug_reaction_cc(DrugMentions, ReactionMention, CC) :-
+	DrugMentions = [_|_],
+	!,
+	(   (var(ReactionMention); ReactionMention==all)
+	->  ReactionLit = literal(Reaction)
+	;   ReactionLit = literal(exact(ReactionMention), Reaction)
+	),
+	findall(cc(Report,Drug,Reaction),
+	      (	  member(Drug, DrugMentions),
+		  rdf(DrugUse, aers:drugname, literal(Drug)),
+		  rdf(Report, aers:drug, DrugUse),
+		  rdf(Report, aers:reaction, ReactionLit)
+	      ),
+	      CC0),
+	sort(CC0, CC).
+
+
 report_obj(R, JSON) :-
 	resource_CBD(rdf, R, Graph),
 	graph_json(Graph, JSON).
 
-
+cc_json(cc(Report,Drug,Reaction),
+	json([report=Report,drug=Drug,reaction=Reaction])).
 
 
diff --git a/lib/aers_report.pl b/lib/aers_report.pl
index 5e2929f..3dc944c 100644
--- a/lib/aers_report.pl
+++ b/lib/aers_report.pl
@@ -78,10 +78,11 @@ reaction_count(Reaction, Count) :-
 	virgil_cache(reaction(Reaction), Count),
 	!.
 reaction_count(Reaction, Count) :-
-	setof(R-D, (report([], [Reaction], [], R),
-		    report_drug_name(R, D)
-		   ),
-	      Es),
+	findall(R-D, (report([], [Reaction], [], R),
+		      report_drug_name(R, D)
+		     ),
+		Es0),
+	sort(Es0, Es),
 	length(Es, Count),
 	assert(virgil_cache(reaction(Reaction), Count)).
 
@@ -91,7 +92,8 @@ cc_count(Count) :-
 	virgil_cache(cc, Count),
 	!.
 cc_count(Count) :-
-	setof(t(R,D,E), report_drug_reaction([], R, D, E), As),
+	findall(t(R,D,E), report_drug_reaction([], R, D, E), As0),
+	sort(As0, As),
 	length(As, Count),
 	assert(virgil_cache(cc, Count)).