Examples with MatchTest org.edamontology.edammap.core.benchmarking.MatchTest used on opensource projects

Example 1 with MatchTest

use of org.edamontology.edammap.core.benchmarking.MatchTest in project edammap by edamontology.

the class Txt method out.

static void out(QueryType type, PrintStream ps, Map<EdamUri, Concept> concepts, List<Query> queries, List<MappingTest> mappings) throws IOException {
    ps.print("query_id");
    ps.print(SEP);
    ps.print("query_name");
    ps.print(SEP);
    ps.print("edam_branch");
    ps.print(SEP);
    ps.print("edam_uri");
    ps.print(SEP);
    ps.print("edam_label");
    ps.print(SEP);
    ps.print("edam_obsolete");
    ps.print(SEP);
    ps.print("best_one_query");
    ps.print(SEP);
    ps.print("best_one_edam");
    ps.print(SEP);
    ps.print("best_one_score");
    ps.print(SEP);
    ps.print("without_path_score");
    ps.print(SEP);
    ps.print("score");
    ps.print(SEP);
    ps.print("test");
    ps.println();
    for (int i = 0; i < queries.size(); ++i) {
        Query query = queries.get(i);
        MappingTest mapping = mappings.get(i);
        for (Branch branch : Branch.values()) {
            for (MatchTest matchTest : mapping.getMatches(branch)) {
                Match match = matchTest.getMatch();
                Concept concept = concepts.get(match.getEdamUri());
                ps.print(query.getId() != null ? query.getId() : "");
                ps.print(SEP);
                ps.print(query.getName() != null ? query.getName() : "");
                ps.print(SEP);
                ps.print(branch);
                ps.print(SEP);
                ps.print(match.getEdamUri());
                ps.print(SEP);
                ps.print(concept.getLabel());
                ps.print(SEP);
                ps.print(concept.isObsolete());
                ps.print(SEP);
                ps.print(match.getQueryMatch().getType().name());
                ps.print(SEP);
                ps.print(match.getConceptMatch().getType().name());
                ps.print(SEP);
                ps.print(match.getBestOneScore() > -1 ? match.getBestOneScore() : "");
                ps.print(SEP);
                ps.print(match.getWithoutPathScore() > -1 ? match.getWithoutPathScore() : "");
                ps.print(SEP);
                ps.print(match.getScore());
                ps.print(SEP);
                ps.print(matchTest.getTest().name());
                ps.println();
            }
        }
    }
}

Example 2 with MatchTest

use of org.edamontology.edammap.core.benchmarking.MatchTest in project edammap by edamontology.

the class Report method writeMatches.

private static void writeMatches(ScoreArgs scoreArgs, Writer writer, Map<EdamUri, Concept> concepts, Query query, List<Publication> publications, MappingTest mapping) throws IOException {
    for (Branch branch : Branch.values()) {
        List<MatchTest> matches = mapping.getMatches(branch);
        if (matches.isEmpty())
            continue;
        writer.write("\t\t<div class=\"branch " + branch + "\">\n");
        writer.write("\t\t\t<h3>" + branch + "</h3>\n");
        for (MatchTest matchTest : matches) {
            Match match = matchTest.getMatch();
            writer.write("\t\t\t<div class=\"match " + matchTest.getTest().name() + "\">\n");
            writer.write("\t\t\t\t<div class=\"match-div\">\n");
            writeConcept(writer, concepts, match);
            writeQueryMatch(writer, query, publications, match.getQueryMatch(), true);
            writer.write("\t\t\t\t\t<div class=\"type\">" + match.getConceptMatch().getType() + "</div>\n");
            writeScore(scoreArgs, writer, branch, match);
            writer.write("\t\t\t\t</div>\n");
            List<MatchAverageStats> matchAverageStats = match.getMatchAverageStats();
            if (matchAverageStats != null && !matchAverageStats.isEmpty()) {
                // TODO
                Concept concept = concepts.get(match.getEdamUri());
                writer.write("\t\t\t\t<div class=\"details-div\">\n");
                writer.write("\t\t\t\t\t<div class=\"details\" tabindex=\"0\"></div>\n");
                writer.write("\t\t\t\t\t<div class=\"details-box\" tabindex=\"0\">\n");
                for (MatchAverageStats mas : matchAverageStats) {
                    writer.write("\t\t\t\t\t\t<div><div>");
                    writeQueryMatch(writer, query, publications, mas.getQueryMatch(), false);
                    writer.write("<br>" + percent(mas.getQueryMatch().getScore()) + "</div><div>");
                    ConceptMatchType conceptType = mas.getConceptMatch().getType();
                    writer.write("<span>" + conceptType + "</span>");
                    if (conceptType != ConceptMatchType.definition && conceptType != ConceptMatchType.comment && conceptType != ConceptMatchType.none) {
                        writer.write("<br>" + conceptMatchString(concept, mas.getConceptMatch()));
                    }
                    writer.write("<br>" + percent(mas.getConceptMatch().getScore()) + "</div><div>");
                    writer.write("<span>" + percent(mas.getScore()) + "</span></div></div>\n");
                }
                writer.write("\t\t\t\t\t</div>\n");
                writer.write("\t\t\t\t</div>\n");
            }
            writer.write("\t\t\t</div>\n");
        }
        writer.write("\t\t</div>\n");
    }
}