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

Example 1 with Tool

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

the class QueryLoader method get.

public static List<Query> get(String queryPath, QueryType type, Map<EdamUri, Concept> concepts, int timeout, String userAgent) throws IOException, ParseException {
    if (type == QueryType.server) {
        throw new IllegalArgumentException("Query of type \"" + QueryType.server.name() + "\" is not loadable from path, but has to be provided");
    }
    List<? extends InputType> inputs;
    if (type == QueryType.biotools) {
        inputs = Json.load(queryPath, type, timeout, userAgent);
    } else if (type == QueryType.biotools14) {
        inputs = Xml.load(queryPath, type, timeout, userAgent);
    } else {
        inputs = Csv.load(queryPath, type, timeout, userAgent);
    }
    Set<Query> queries = new LinkedHashSet<>();
    String filename = new File(queryPath).getName();
    for (InputType input : inputs) {
        switch(type) {
            case generic:
                queries.add(getGeneric((Generic) input, concepts, filename));
                break;
            case SEQwiki:
                queries.add(getSEQwiki((SEQwiki) input, concepts, filename));
                break;
            case msutils:
                queries.add(getMsutils((Msutils) input, concepts, filename));
                break;
            case Bioconductor:
                queries.add(getBioconductor((Bioconductor) input, concepts));
                break;
            case biotools14:
                queries.add(getBiotools14((Biotools14) input, concepts, filename));
                break;
            case biotools:
                queries.add(getBiotools((Tool) input, concepts, 0, 0, filename));
                break;
            case server:
                break;
        }
    }
    return new ArrayList<>(queries);
}

Example 2 with Tool

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

the class Json method outputBiotools.

public static void outputBiotools(Writer writer, List<Tool> tools) throws IOException {
    ObjectMapper mapper = new ObjectMapper();
    JsonGenerator generator = createGenerator(writer, null, mapper);
    mapper.setSerializationInclusion(Include.NON_EMPTY);
    generator.writeStartObject();
    generator.writeNumberField("count", tools.size());
    generator.writeFieldName("list");
    generator.writeStartArray();
    for (Tool tool : tools) {
        generator.writeObject(tool);
    }
    generator.writeEndArray();
    generator.writeEndObject();
    generator.close();
}

Example 3 with Tool

use of org.edamontology.edammap.core.input.json.Tool 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);
}