VICC results, see #1

Dockerfile

@@ -2,14 +2,19 @@ FROM swipl:7.5.12
 MAINTAINER Chris Mungall <[email protected]>
 
 RUN apt-get update && apt-get -y install make curl
-RUN mkdir /data && curl -L http://purl.obolibrary.org/obo/mondo.owl -o /data/mondo.owl && curl -L http://purl.obolibrary.org/obo/ncit/neoplasm-core.owl -o /data/neoplasm-core.owl
+RUN mkdir /data && curl -L http://purl.obolibrary.org/obo/mondo.owl -o /data/mondo.owl && curl -L http://purl.obolibrary.org/obo/doid.owl -o /data/doid.owl && curl -L http://purl.obolibrary.org/obo/ncit/neoplasm-core.owl -o /data/neoplasm-core.owl
 
 ADD ./prolog/ /tools/prolog
 ADD ./bin/ /tools/bin
 ADD ./utf8.pl /tools/
+ADD ./install.pl /tools/
+ADD ./pack.pl /tools/
+ADD ./tests/data/inputs.txt /tools/
 WORKDIR /tools
-RUN swipl -g "Opts=[interactive(false)],pack_install(sparqlprog,[url('https://github.com/cmungall/index_util/archive/v0.0.2.zip')|Opts]),pack_install(sparqlprog,Opts),pack_install(rdf_matcher,Opts),halt"
+RUN swipl -l install -g install_requirements,halt
 ENV PATH "/tools/bin:$PATH"
 
+RUN swipl -G0  -p library=/tools/prolog -l /tools/utf8.pl /tools/bin/neoplasmer -X .cache -i /data/mondo.owl -i /data/doid.owl -i /data/neoplasm-core.owl inputs.txt
+
 EXPOSE ${PORT}
 CMD swipl -p library=prolog ./bin/neoplasmer -h

Makefile

@@ -8,14 +8,14 @@
 #include ../Makefile.inc
 
 SWIPL = swipl  -L0 -G0 -T0  -p library=prolog
-all: test
+all: tmp test
 
 check:
 install:
 clean:
 
 
-test:
+test: tmp
 	$(SWIPL) -l tests/tests.pl -g run_tests,halt
 
 bigtest:
@@ -27,6 +27,8 @@ coverage:
 t-%:
 	$(SWIPL) -l tests/$*_test.pl -g run_tests,halt
 
+tmp:
+	mkdir $@
 
 # --------------------
 # Docker

bin/neoplasmer

@@ -193,14 +193,19 @@ main(Argv) :-
 
 
 parse_and_match(File) :-
-        csv_read_file(File,Rows,[]),
+        csv_read_file(File,Rows,[match_arity(false)]),
         maplist(parse_row,Rows).
 
 parse_row(Row) :-
+        Opts=[format(tsv)],
         Row =.. [_Pred,Term|_],
         G = term_best_match(Term,_,_,_),
-        forall(G,
-               write_result_wrap(G,[format(tsv)])).
+        findall(G,G,Gs),
+        (   Gs=[]
+        ->  write_result_wrap(term_best_match(Term,no_match,'n/a',none),Opts)
+        ;   forall(member(G,Gs),
+                   write_result_wrap(G,Opts))).
+
 
 
 write_result_wrap(G,Opts) :-

install.pl

@@ -0,0 +1,12 @@
+
+install_requirements :-
+        ensure_loaded(pack),
+        % https://swi-prolog.discourse.group/t/www-swi-prolog-org-goes-https/811/3
+        ensure_loaded(library(prolog_pack)),
+        set_setting(prolog_pack:server, 'https://www.swi-prolog.org/pack/'),
+        Opts=[interactive(false)],
+        requires(X),
+        pack_install(X, Opts),
+        fail.
+install_requirements.
+

neoplasmer.sh

@@ -1,3 +1,3 @@
 #!/bin/sh
-docker run -p 9055:9055 -e PORT=9055 -v $PWD:/work -w /work --rm -ti cmungall/neoplasmer swipl -G0  -p library=/tools/prolog -l /tools/utf8.pl /tools/bin/neoplasmer -X .cache -i /data/mondo.owl -i /data/neoplasm-core.owl "$@"
+docker run -p 9055:9055 -e PORT=9055 -v $PWD:/work -w /work  --rm -ti cmungall/neoplasmer swipl -G0  -p library=/tools/prolog -l /tools/utf8.pl /tools/bin/neoplasmer -X .cache -i /data/mondo.owl -i /data/doid.owl -i /data/neoplasm-core.owl "$@"
 

pack.pl

@@ -1,6 +1,6 @@
 name(neoplasmer).
 title('neoplasm entity recognition').
-version('0.0.1').
+version('0.0.2').
 author('Chris Mungall','[email protected]').
 packager('Chris Mungall','[email protected]').
 home('https://github.com/cmungall/neoplasmER').

prolog/neoplasmer.pl

@@ -72,6 +72,7 @@
 %! term_best_match(+Term, ?MatchCls, ?MatchScore, ?MatchClsPrefix) is nondet
 term_best_match(V, C, S, P) :-
         debug(matcher,'Matching: ~w',[V]),
+        % succeeds once for every value of P
         setof(C-S,term_match_score(V, C, S, P),Pairs),
         member(C-S,Pairs),
         \+ ((member(_-S2,Pairs),S2>S)).