Examples with Biotools org.edamontology.edammap.core.input.json.Biotools used on opensource projects

Example 1 with Biotools

use of org.edamontology.edammap.core.input.json.Biotools in project edammap by edamontology.

the class Util method biotoolsFull.

private static void biotoolsFull(String outputPath, FetcherArgs fetcherArgs, boolean dev) throws IOException {
    logger.info("Make full {}bio.tools JSON to {}", dev ? "dev." : "", outputPath);
    String api = "https://" + (dev ? "dev." : "") + "bio.tools/api/tool";
    Path output = FetcherCommon.outputPath(outputPath);
    ObjectMapper mapper = new ObjectMapper();
    mapper.enable(SerializationFeature.INDENT_OUTPUT);
    mapper.enable(SerializationFeature.CLOSE_CLOSEABLE);
    Biotools biotoolsFull = new Biotools();
    int count = 0;
    String next = "?page=1";
    while (next != null) {
        try (InputStream is = Input.newInputStream(api + next + "&format=json", false, fetcherArgs.getTimeout(), fetcherArgs.getPrivateArgs().getUserAgent())) {
            Biotools biotools = mapper.readValue(is, Biotools.class);
            biotoolsFull.addTools(biotools.getList());
            biotoolsFull.setCount(biotools.getCount());
            count += biotools.getList().size();
            next = biotools.getNext();
        } catch (Exception e) {
            logger.error("Exception!", e);
            break;
        }
    }
    mapper.writeValue(output.toFile(), biotoolsFull);
    if (count != biotoolsFull.getCount()) {
        logger.error("Got {} entries instead of advertised {}", count, biotoolsFull.getCount());
    }
    logger.info("Made bio.tools JSON with {} entries", count);
}

Example 2 with Biotools

use of org.edamontology.edammap.core.input.json.Biotools in project edammap by edamontology.

the class Json method outputBiotools.

public static void outputBiotools(CoreArgs args, String queryPath, Path biotoolsPath, Map<EdamUri, Concept> concepts, Results results) throws IOException {
    ObjectMapper mapper = new ObjectMapper();
    mapper.enable(SerializationFeature.INDENT_OUTPUT);
    mapper.enable(SerializationFeature.CLOSE_CLOSEABLE);
    mapper.setSerializationInclusion(Include.NON_EMPTY);
    Biotools biotools = null;
    try (InputStream is = Input.newInputStream(queryPath, true, args.getFetcherArgs().getTimeout(), args.getFetcherArgs().getPrivateArgs().getUserAgent())) {
        biotools = mapper.readValue(is, Biotools.class);
    }
    if (biotools.getList().size() != results.getMappings().size()) {
        throw new RuntimeException("Number of results (" + results.getMappings().size() + ") does not correspond to number of tools (" + biotools.getList().size() + ") from " + queryPath);
    }
    for (int i = 0; i < biotools.getList().size(); ++i) {
        Tool tool = biotools.getList().get(i);
        MappingTest mapping = results.getMappings().get(i);
        if (tool.getBiotoolsID() != null && !tool.getBiotoolsID().equals(mapping.getId())) {
            throw new RuntimeException("Tool ID from " + queryPath + " (" + tool.getBiotoolsID() + ") does not correspond to ID from results (" + mapping.getId() + ")");
        }
        if (!tool.getName().equals(mapping.getName())) {
            throw new RuntimeException("Tool name from " + queryPath + " (" + tool.getName() + ") does not correspond to name from results (" + mapping.getName() + ")");
        }
    }
    for (int i = 0; i < biotools.getList().size(); ++i) {
        Tool tool = biotools.getList().get(i);
        MappingTest mapping = results.getMappings().get(i);
        addAnnotations(args, tool, mapping, concepts);
    }
    mapper.writeValue(biotoolsPath.toFile(), biotools);
}

Example 3 with Biotools

use of org.edamontology.edammap.core.input.json.Biotools in project edammap by edamontology.

the class BiotoolsFull method get.

public static int get(String outputPath, FetcherArgs fetcherArgs, boolean dev, boolean stderr) throws IOException {
    logger.info("Make full {}bio.tools JSON to {}", dev ? "dev." : "", outputPath);
    String api = "https://" + (dev ? "dev." : "") + "bio.tools/api/tool";
    Path output = PubFetcher.outputPath(outputPath);
    ObjectMapper mapper = new ObjectMapper();
    mapper.enable(SerializationFeature.INDENT_OUTPUT);
    mapper.enable(SerializationFeature.CLOSE_CLOSEABLE);
    Biotools biotoolsFull = new Biotools();
    int count = 0;
    boolean error = false;
    String next = "?page=1";
    int page = 0;
    long start = System.currentTimeMillis();
    while (next != null) {
        ++page;
        try (InputStream is = Input.newInputStream(api + next + "&format=json", false, fetcherArgs.getTimeout(), fetcherArgs.getPrivateArgs().getUserAgent())) {
            Biotools biotools = mapper.readValue(is, Biotools.class);
            if (stderr) {
                System.err.print(PubFetcher.progress(page, biotools.getCount() / 10 + 1, start) + "  \r");
            }
            biotoolsFull.addTools(biotools.getList());
            biotoolsFull.setCount(biotools.getCount());
            count += biotools.getList().size();
            next = biotools.getNext();
        } catch (Exception e) {
            logger.error("Exception at " + next + "!", e);
            error = true;
            break;
        }
    }
    mapper.writeValue(output.toFile(), biotoolsFull);
    if (count != biotoolsFull.getCount()) {
        logger.error("Got {} {}bio.tools entries instead of advertised {}", count, dev ? "dev." : "", biotoolsFull.getCount());
    }
    logger.info("Made {}bio.tools JSON with {} entries", dev ? "dev." : "", count);
    if (count != biotoolsFull.getCount()) {
        throw new RuntimeException("Got " + count + " " + (dev ? "dev." : "") + "bio.tools entries instead of advertised " + biotoolsFull.getCount());
    } else if (error) {
        throw new RuntimeException("Error getting full " + (dev ? "dev." : "") + "bio.tools content");
    }
    return count;
}