Examples with Param org.edamontology.edammap.core.output.Param used on opensource projects

Example 1 with Param

use of org.edamontology.edammap.core.output.Param in project edammap by edamontology.

the class Cli method run.

private static void run(Version version) throws IOException, ParseException {
    List<Param> paramsMain = new ArrayList<>();
    paramsMain.add(new Param("Ontology file", CliArgs.EDAM, new File(args.getEdam()).getName(), "https://github.com/edamontology/edamontology/tree/master/releases"));
    if (Input.isProtocol(args.getQuery())) {
        paramsMain.add(new Param("Query file", CliArgs.QUERY, args.getQuery(), args.getQuery()));
    } else {
        paramsMain.add(new Param("Query file", CliArgs.QUERY, new File(args.getQuery()).getName()));
    }
    paramsMain.add(new Param("Type", CliArgs.TYPE, args.getType().toString()));
    paramsMain.add(new Param("Output file", CliArgs.OUTPUT, new File(args.getOutput()).getName()));
    paramsMain.add(new Param("Report file", CliArgs.REPORT, new File(args.getReport()).getName()));
    paramsMain.add(new Param("Report page size", CliArgs.REPORT_PAGE_SIZE, args.getReportPageSize(), 0.0, null));
    paramsMain.add(new Param("Report pagination size", CliArgs.REPORT_PAGINATION_SIZE, args.getReportPaginationSize(), 0.0, null));
    paramsMain.add(new Param("Number of threads", CliArgs.THREADS, args.getThreads(), 0.0, null));
    Output output = new Output(args.getOutput(), args.getReport(), false);
    stopwords = PreProcessor.getStopwords(args.getPreProcessorArgs().getStopwords());
    processor = new Processor(args.getProcessorArgs());
    idf = null;
    if (args.getPreProcessorArgs().isStemming()) {
        if (args.getProcessorArgs().getIdfStemmed() != null && !args.getProcessorArgs().getIdfStemmed().isEmpty()) {
            idf = new Idf(args.getProcessorArgs().getIdfStemmed());
        }
    } else {
        if (args.getProcessorArgs().getIdf() != null && !args.getProcessorArgs().getIdf().isEmpty()) {
            idf = new Idf(args.getProcessorArgs().getIdf());
        }
    }
    logger.info("Loading concepts");
    Map<EdamUri, Concept> concepts = Edam.load(args.getEdam());
    logger.info("Processing {} concepts", concepts.size());
    processedConcepts = processor.getProcessedConcepts(concepts, args.getMapperArgs().getIdfArgs(), args.getMapperArgs().getMultiplierArgs(), new PreProcessor(args.getPreProcessorArgs(), stopwords));
    logger.info("Loading queries");
    queries = QueryLoader.get(args.getQuery(), args.getType(), concepts, args.getFetcherArgs().getTimeout(), args.getFetcherArgs().getPrivateArgs().getUserAgent());
    publications = new ArrayList<>(queries.size());
    webpages = new ArrayList<>(queries.size());
    docs = new ArrayList<>(queries.size());
    mappings = new ArrayList<>(queries.size());
    for (int i = 0; i < queries.size(); ++i) {
        publications.add(null);
        webpages.add(null);
        docs.add(null);
        mappings.add(null);
    }
    start = System.currentTimeMillis();
    logger.info("Start: {}", Instant.ofEpochMilli(start));
    logger.info("Starting mapper threads");
    for (int i = 0; i < args.getThreads(); ++i) {
        Thread t = new Thread(new Cli());
        t.setDaemon(true);
        t.start();
    }
    synchronized (lock) {
        while (!lockDone || numThreads > 0) {
            try {
                lock.wait();
            } catch (InterruptedException e) {
                // TODO exit threads cleanly? give timeout for threads to exit? close db? print that exiting and waiting for threads to terminate?
                logger.error("Exception!", e);
                System.exit(1);
            }
        }
    }
    logger.info("All mapper threads stopped");
    long stop = System.currentTimeMillis();
    logger.info("Stop: {}", Instant.ofEpochMilli(stop));
    logger.info("Mapping took {}s", (stop - start) / 1000.0);
    Results results = Benchmark.calculate(queries, mappings);
    logger.info("Outputting results");
    output.output(args, paramsMain, args.getType(), args.getReportPageSize(), args.getReportPaginationSize(), concepts, queries, webpages, docs, publications, results, start, stop, version);
    logger.info("{} : {}", results.toStringMeasure(Measure.recall), Measure.recall);
    logger.info("{} : {}", results.toStringMeasure(Measure.AveP), Measure.AveP);
}

Example 2 with Param

use of org.edamontology.edammap.core.output.Param in project edammap by edamontology.

the class Server method run.

private static void run() throws IOException, ParseException {
    paramsMain.add(new Param("Ontology file", ServerArgs.EDAM, new File(args.getEdam()).getName(), "https://github.com/edamontology/edamontology/tree/master/releases"));
    for (Stopwords stopwords : Stopwords.values()) {
        stopwordsAll.put(stopwords, PreProcessor.getStopwords(stopwords));
    }
    processor = new Processor(args.getProcessorArgs());
    if (args.getProcessorArgs().getIdf() != null && !args.getProcessorArgs().getIdf().isEmpty()) {
        idf = new Idf(args.getProcessorArgs().getIdf());
    }
    if (args.getProcessorArgs().getIdfStemmed() != null && !args.getProcessorArgs().getIdfStemmed().isEmpty()) {
        idfStemmed = new Idf(args.getProcessorArgs().getIdfStemmed());
    }
    logger.info("Loading concepts");
    concepts = Edam.load(args.getEdam());
    logger.info("Configuring server");
    final ResourceConfig rc = new ResourceConfig().packages("org.edamontology.edammap.server");
    // TODO .property(JsonGenerator.PRETTY_PRINTING, true);
    HttpServer httpServer = GrizzlyHttpServerFactory.createHttpServer(URI.create(args.getBaseUri() + "/" + args.getPath() + "/api"), rc, false);
    final StaticHttpHandler filesHttpHandler = new StaticHttpHandler(args.getFiles());
    filesHttpHandler.setDirectorySlashOff(true);
    httpServer.getServerConfiguration().addHttpHandler(filesHttpHandler, "/" + args.getPath() + "/*");
    httpServer.getServerConfiguration().addHttpHandler(new HttpHandler() {

        @Override
        public void service(Request request, Response response) throws Exception {
            // TODO replace null with request.getParameterMap()
            String responseText = Resource.runGet(null, request);
            response.setContentType(MediaType.TEXT_HTML);
            response.setContentLength(responseText.length());
            response.getWriter().write(responseText);
        }
    }, "/" + args.getPath() + "/");
    if (args.getLog() != null) {
        Path accessDir = Paths.get(args.getLog() + "/access");
        if (!Files.exists(accessDir)) {
            Files.createDirectory(accessDir);
        }
        final AccessLogBuilder builder = new AccessLogBuilder(accessDir + "/edammap-access.log");
        builder.rotatedDaily();
        // builder.format(ApacheLogFormat.COMBINED); // TODO
        builder.instrument(httpServer.getServerConfiguration());
    }
    logger.info("Starting server");
    httpServer.start();
    logger.info("{} has started", version.getName());
}