Examples with EdamUri org.edamontology.edammap.core.edam.EdamUri used on opensource projects

Example 1 with EdamUri

use of org.edamontology.edammap.core.edam.EdamUri in project edammap by edamontology.

the class Report method writeConcept.

private static void writeConcept(Writer writer, Map<EdamUri, Concept> concepts, Match match) throws IOException {
    EdamUri edamUri = match.getEdamUri();
    // TODO
    Concept concept = concepts.get(edamUri);
    writer.write("\t\t\t\t\t<div class=\"concept\">");
    if (concept.isObsolete()) {
        writer.write("<span class=\"obsolete\">");
    }
    writer.write("<strong>" + FetcherCommon.getLinkHtml(edamUri.toString(), concept.getLabel() + " (" + edamUri.getNrString() + ")") + "</strong>");
    if (match.getConceptMatch().getType() != ConceptMatchType.label && match.getConceptMatch().getType() != ConceptMatchType.none) {
        writer.write(" (" + conceptMatchString(concept, match.getConceptMatch()) + ")");
    }
    if (concept.isObsolete()) {
        writer.write("</span>");
    }
    writeParentsChildren(writer, concepts, match.getParents(), "Child of");
    writeParentsChildren(writer, concepts, match.getParentsAnnotation(), "Child of annotation");
    writeParentsChildren(writer, concepts, match.getParentsRemainingAnnotation(), "Child of excluded annotation");
    writeParentsChildren(writer, concepts, match.getChildren(), "Parent of");
    writeParentsChildren(writer, concepts, match.getChildrenAnnotation(), "Parent of annotation");
    writeParentsChildren(writer, concepts, match.getChildrenRemainingAnnotation(), "Parent of excluded annotation");
    writer.write("</div>\n");
}

Example 2 with EdamUri

use of org.edamontology.edammap.core.edam.EdamUri 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 3 with EdamUri

use of org.edamontology.edammap.core.edam.EdamUri in project edammap by edamontology.

the class QueryLoader method getBiotools.

private static Query getBiotools(ToolInput tool, Map<EdamUri, Concept> concepts) {
    List<Link> webpageUrls = new ArrayList<>();
    addLink(tool.getHomepage(), "Homepage", false, webpageUrls);
    webpageUrls.addAll(linksJson(tool.getLink().stream(), Arrays.asList("mirror", "repository", "browser"), false));
    List<Link> docUrls = linksJson(tool.getDocumentation().stream(), Arrays.asList("general", "manual", "api documentation", "training material"), false);
    List<PublicationIdsQuery> publicationIds = new ArrayList<>();
    for (Publication publication : tool.getPublication()) {
        addPublicationId(publication.getPmid(), publication.getPmcid(), publication.getDoi(), BIOTOOLS, publication.getType(), false, publicationIds);
    }
    Set<EdamUri> annotations = new LinkedHashSet<>();
    annotations.addAll(edamUrisJson(tool.getTopic().stream(), concepts));
    for (Function function : tool.getFunction()) {
        annotations.addAll(edamUrisJson(function.getOperation().stream(), concepts));
        for (InputOutput input : function.getInput()) {
            annotations.addAll(edamUrisJson(Collections.singletonList(input.getData()).stream(), concepts));
            if (input.getFormat() != null) {
                annotations.addAll(edamUrisJson(input.getFormat().stream(), concepts));
            }
        }
        for (InputOutput output : function.getOutput()) {
            annotations.addAll(edamUrisJson(Collections.singletonList(output.getData()).stream(), concepts));
            if (output.getFormat() != null) {
                annotations.addAll(edamUrisJson(output.getFormat().stream(), concepts));
            }
        }
    }
    return new Query(tool.getId().trim(), tool.getName().trim(), null, tool.getDescription().trim(), webpageUrls, docUrls, publicationIds, annotations);
}

Example 4 with EdamUri

use of org.edamontology.edammap.core.edam.EdamUri in project edammap by edamontology.

the class Resource method runPost.

private Response runPost(MultivaluedMap<String, String> params, Request request) throws IOException, ParseException, URISyntaxException {
    logger.info("POST {} from {}", params, request.getRemoteAddr());
    long start = System.currentTimeMillis();
    logger.info("Start: {}", Instant.ofEpochMilli(start));
    CoreArgs coreArgs = new CoreArgs();
    ParamParse.parseParams(params, coreArgs);
    coreArgs.setProcessorArgs(Server.args.getProcessorArgs());
    coreArgs.getFetcherArgs().setPrivateArgs(Server.args.getFetcherPrivateArgs());
    ServerInput serverInput = new ServerInput(ParamParse.getParamString(params, "name"), ParamParse.getParamString(params, "keywords"), ParamParse.getParamString(params, "description"), ParamParse.getParamString(params, "webpage-urls"), ParamParse.getParamString(params, "doc-urls"), ParamParse.getParamString(params, "publication-ids"), ParamParse.getParamString(params, "annotations"));
    if (serverInput.getName() != null && serverInput.getName().length() > MAX_NAME_LENGTH) {
        throw new IllegalArgumentException("Name length (" + serverInput.getName().length() + ") is greater than maximum allowed (" + MAX_NAME_LENGTH + ")");
    }
    if (serverInput.getKeywords() != null && serverInput.getKeywords().length() > MAX_KEYWORDS_LENGTH) {
        throw new IllegalArgumentException("Keywords length (" + serverInput.getKeywords().length() + ") is greater than maximum allowed (" + MAX_KEYWORDS_LENGTH + ")");
    }
    if (serverInput.getDescription() != null && serverInput.getDescription().length() > MAX_DESCRIPTION_LENGTH) {
        throw new IllegalArgumentException("Description length (" + serverInput.getDescription().length() + ") is greater than maximum allowed (" + MAX_DESCRIPTION_LENGTH + ")");
    }
    if (serverInput.getWebpageUrls() != null && serverInput.getWebpageUrls().length() > MAX_LINKS_LENGTH) {
        throw new IllegalArgumentException("Webpage URLs length (" + serverInput.getWebpageUrls().length() + ") is greater than maximum allowed (" + MAX_LINKS_LENGTH + ")");
    }
    if (serverInput.getDocUrls() != null && serverInput.getDocUrls().length() > MAX_LINKS_LENGTH) {
        throw new IllegalArgumentException("Doc URLs length (" + serverInput.getDocUrls().length() + ") is greater than maximum allowed (" + MAX_LINKS_LENGTH + ")");
    }
    if (serverInput.getPublicationIds() != null && serverInput.getPublicationIds().length() > MAX_PUBLICATION_IDS_LENGTH) {
        throw new IllegalArgumentException("Publication IDs length (" + serverInput.getPublicationIds().length() + ") is greater than maximum allowed (" + MAX_PUBLICATION_IDS_LENGTH + ")");
    }
    if (serverInput.getAnnotations() != null && serverInput.getAnnotations().length() > MAX_ANNOTATIONS_LENGTH) {
        throw new IllegalArgumentException("Annotations length (" + serverInput.getAnnotations().length() + ") is greater than maximum allowed (" + MAX_ANNOTATIONS_LENGTH + ")");
    }
    String uuid;
    String uuidDir;
    do {
        uuid = Server.version.getVersion() + "/" + UUID.randomUUID().toString();
        uuidDir = Server.args.getFiles() + "/" + uuid;
    } while (Files.exists(Paths.get(uuidDir)));
    Files.createDirectory(Paths.get(uuidDir));
    serverInput.setId(uuid);
    logger.info("UUID: {}", uuid);
    Output output = new Output(uuidDir + "/results.txt", uuidDir, true);
    // TODO params to choose if HTML or TXT output desired
    PreProcessor preProcessor = new PreProcessor(coreArgs.getPreProcessorArgs(), Server.stopwordsAll.get(coreArgs.getPreProcessorArgs().getStopwords()));
    logger.info("Processing {} concepts", Server.concepts.size());
    Map<EdamUri, ConceptProcessed> processedConcepts = Server.processor.getProcessedConcepts(Server.concepts, coreArgs.getMapperArgs().getIdfArgs(), coreArgs.getMapperArgs().getMultiplierArgs(), preProcessor);
    logger.info("Loading query");
    Query query = QueryLoader.fromServer(serverInput, Server.concepts, MAX_KEYWORDS_SIZE, MAX_LINKS_SIZE, MAX_PUBLICATION_IDS_SIZE);
    Idf idf;
    if (coreArgs.getPreProcessorArgs().isStemming()) {
        idf = Server.idfStemmed;
    } else {
        idf = Server.idf;
    }
    QueryProcessed processedQuery = Server.processor.getProcessedQuery(query, QueryType.server, preProcessor, idf, coreArgs.getFetcherArgs());
    logger.info("Mapping query");
    Mapping mapping = new Mapper(processedConcepts).map(query, processedQuery, coreArgs.getMapperArgs());
    List<Query> queries = Collections.singletonList(query);
    List<List<Webpage>> webpages = Collections.singletonList(processedQuery.getWebpages());
    List<List<Webpage>> docs = Collections.singletonList(processedQuery.getDocs());
    List<List<Publication>> publications = Collections.singletonList(processedQuery.getPublications());
    List<Mapping> mappings = Collections.singletonList(mapping);
    Results results = Benchmark.calculate(queries, mappings);
    long stop = System.currentTimeMillis();
    logger.info("Stop: {}", Instant.ofEpochMilli(stop));
    logger.info("Mapping took {}s", (stop - start) / 1000.0);
    logger.info("Outputting results");
    output.output(coreArgs, Server.paramsMain, QueryType.server, 1, 1, Server.concepts, queries, webpages, docs, publications, results, start, stop, Server.version);
    URI location = new URI("/" + Server.args.getPath() + "/" + uuid + "/");
    logger.info("POSTED {}", location);
    return Response.seeOther(location).build();
}

Example 5 with EdamUri

use of org.edamontology.edammap.core.edam.EdamUri in project edammap by edamontology.

the class Processor method getProcessedConcepts.

public Map<EdamUri, ConceptProcessed> getProcessedConcepts(Map<EdamUri, Concept> concepts, IdfArgs idfArgs, MultiplierArgs multiplierArgs, PreProcessor preProcessor) {
    Map<EdamUri, ConceptProcessed> processedConcepts = new LinkedHashMap<>();
    IdfMake idfMake = new IdfMake();
    for (Map.Entry<EdamUri, Concept> concept : concepts.entrySet()) {
        processedConcepts.put(concept.getKey(), processConcept(concept.getValue(), idfMake, preProcessor));
    }
    Idf idf = new Idf(idfMake.getIdf());
    for (ConceptProcessed processedConcept : processedConcepts.values()) {
        processConceptIdf(processedConcept, idf);
    }
    for (ConceptProcessed processedConcept : processedConcepts.values()) {
        anonymizeProcessedConcept(processedConcept, idfArgs, multiplierArgs);
    }
    return processedConcepts;
}