Example usage for com.google.gson JsonElement getAsJsonObject

List of usage examples for com.google.gson JsonElement getAsJsonObject

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Introduction

In this page you can find the example usage for com.google.gson JsonElement getAsJsonObject.

Prototype

public JsonObject getAsJsonObject()

Source Link

Document

convenience method to get this element as a JsonObject .

Usage

From source file:classes.analysis.non_processed_data.IntermediateData.java

License:Open Source License

public static IntermediateData parseStepGalaxyData(JsonObject step_json_object, JsonObject analysisData,
        String emsuser) {/*from   ww w.  j a  va2 s .co m*/
    IntermediateData step = new IntermediateData("STxxxx." + step_json_object.get("id").getAsString());
    step.setIntermediateDataType("preprocessing_step");
    step.setSoftware(step_json_object.get("tool_id").getAsString());
    step.setSoftwareVersion(step_json_object.get("tool_version").getAsString());
    HashSet<String> used_data = new HashSet<String>();
    if (step_json_object.has("used_data")) {
        for (JsonElement data : step_json_object.get("used_data").getAsJsonArray()) {
            used_data.add(data.getAsString());
        }
    }
    step.setUsedData(used_data.toArray(new String[] {}));

    String prefix = analysisData.get("experiment_id").getAsString() + "/"
            + analysisData.get("analysis_id").getAsString() + "/";
    ArrayList<String> outputs = new ArrayList<String>();
    for (JsonElement output : step_json_object.get("outputs").getAsJsonArray()) {
        outputs.add(prefix + output.getAsJsonObject().get("file").getAsString().replaceAll(" ", "_") + "."
                + output.getAsJsonObject().get("extension").getAsString());
    }
    step.setFilesLocation(outputs.toArray(new String[] {}));

    String description = "Step " + step_json_object.get("id").getAsString() + " in Galaxy history "
            + analysisData.get("history_id").getAsString() + ".\n";
    description += "The tool exited with code " + step_json_object.get("exit_code").getAsString() + "\n";
    description += "Outputs:\n";
    for (JsonElement output : step_json_object.get("outputs").getAsJsonArray()) {
        description += "  - " + output.getAsJsonObject().get("file").getAsString() + " (id:"
                + output.getAsJsonObject().get("id").getAsString() + ")\n";
    }
    step.setResults(description);

    description = "Step inputs:\n";
    for (JsonElement input : step_json_object.get("inputs").getAsJsonArray()) {
        description += "  - " + input.getAsJsonObject().get("file").getAsString() + " (id:"
                + input.getAsJsonObject().get("id").getAsString() + ")\n";
    }
    description += "\n";
    description += "Parameters:\n";
    for (JsonElement input : step_json_object.get("parameters").getAsJsonArray()) {
        description += Step.getParameterDescription(input.getAsJsonObject(), 1);
    }

    step.setSoftwareConfiguration(description);

    Date dateNow = new Date();
    SimpleDateFormat dateFormat = new SimpleDateFormat("yyyyMMdd");
    step.setSubmissionDate(dateFormat.format(dateNow));
    step.setLastEditionDate(dateFormat.format(dateNow));
    step.addOwner(new User(emsuser, ""));
    if (step_json_object.has("step_name")) {
        step.setStepName(step_json_object.get("step_name").getAsString());
    } else {
        step.setStepName(step_json_object.get("tool_id").getAsString());
    }
    step.setStepNumber(step_json_object.get("id").getAsInt());

    return step;
}

From source file:classes.analysis.ProcessedData.java

License:Open Source License

public static ProcessedData parseStepGalaxyData(JsonObject step_json_object, JsonObject analysisData,
        String emsuser) {/*  ww  w. ja  v a 2 s.c  o  m*/
    ProcessedData step = new ProcessedData("STxxxx." + step_json_object.get("id").getAsString());
    step.setProcessedDataType("quantification_step");
    step.setSoftware(step_json_object.get("tool_id").getAsString());
    step.setSoftwareVersion(step_json_object.get("tool_version").getAsString());
    HashSet<String> used_data = new HashSet<String>();
    if (step_json_object.has("used_data")) {
        for (JsonElement data : step_json_object.get("used_data").getAsJsonArray()) {
            used_data.add(data.getAsString());
        }
    }
    step.setUsedData(used_data.toArray(new String[] {}));

    String prefix = analysisData.get("experiment_id").getAsString() + "/"
            + analysisData.get("analysis_id").getAsString() + "/";
    ArrayList<String> outputs = new ArrayList<String>();
    for (JsonElement output : step_json_object.get("outputs").getAsJsonArray()) {
        outputs.add(prefix + output.getAsJsonObject().get("file").getAsString().replaceAll(" ", "_") + "."
                + output.getAsJsonObject().get("extension").getAsString());
    }
    step.setFilesLocation(outputs.toArray(new String[] {}));

    String description = "Step " + step_json_object.get("id").getAsString() + " in Galaxy history "
            + analysisData.get("history_id").getAsString() + ".\n";
    description += "The tool exited with code " + step_json_object.get("exit_code").getAsString() + "\n";
    description += "Outputs:\n";
    for (JsonElement output : step_json_object.get("outputs").getAsJsonArray()) {
        description += "  - " + output.getAsJsonObject().get("file").getAsString() + " (id:"
                + output.getAsJsonObject().get("id").getAsString() + ")\n";
    }
    step.setResults(description);

    description = "Step inputs:\n";
    for (JsonElement input : step_json_object.get("inputs").getAsJsonArray()) {
        description += "  - " + input.getAsJsonObject().get("file").getAsString() + " (id:"
                + input.getAsJsonObject().get("id").getAsString() + ")\n";
    }
    description += "\n";
    description += "Parameters:\n";
    for (JsonElement input : step_json_object.get("parameters").getAsJsonArray()) {
        description += Step.getParameterDescription(input.getAsJsonObject(), 1);
    }

    step.setSoftwareConfiguration(description);

    Date dateNow = new Date();
    SimpleDateFormat dateFormat = new SimpleDateFormat("yyyyMMdd");
    step.setSubmissionDate(dateFormat.format(dateNow));
    step.setLastEditionDate(dateFormat.format(dateNow));
    step.addOwner(new User(emsuser, ""));
    step.setStepName(step_json_object.get("tool_id").getAsString());
    step.setStepNumber(step_json_object.get("id").getAsInt());

    return step;
}

From source file:classes.analysis.Step.java

License:Open Source License

protected static String getParameterDescription(JsonElement parameter, int level) {
    if (parameter.isJsonPrimitive()) {
        return parameter.getAsString() + "\n";
    }/*  w  ww.ja  va 2 s.  c  o  m*/

    if (parameter.isJsonArray()) {
        String description = "";
        String prefix = "";
        for (int i = 0; i < level; i++) {
            prefix += "  ";
        }

        for (JsonElement element : parameter.getAsJsonArray()) {
            description += prefix + Step.getParameterDescription(element, level + 1);
        }

        return description;
    }

    if (parameter.isJsonObject()) {
        String description = "";
        String prefix = "";
        for (int i = 0; i < level; i++) {
            prefix += "  ";
        }

        for (Map.Entry<String, JsonElement> member : parameter.getAsJsonObject().entrySet()) {
            description += prefix + "- " + member.getKey() + ": "
                    + Step.getParameterDescription(member.getValue(), level + 1);
        }
        return description;
    }

    return "";
}

From source file:classes.samples.BioCondition.java

License:Open Source License

private ArrayList<Pair> processElementContent(String templatesDir, String jsonObject)
        throws FileNotFoundException {
    ArrayList<Pair> elements = new ArrayList<Pair>();
    ArrayList<Pair> fields = processTemplateFile(templatesDir + File.separator + "biocondition-form.json");
    JsonObject analysis = new JsonParser().parse(jsonObject).getAsJsonObject();

    elements.add(new Pair("Biological conditions details", "", 0, "title"));
    elements.add(new Pair("", "", 1, "section"));
    for (Pair field : fields) {
        elements.add(new Pair(field.value, this.getJsonElementAsString(analysis.get(field.label)), 2, "field"));
    }//from w  w w.  j a  va  2 s  . c  o m

    elements.add(new Pair("Samples in the analysis", "", 0, "title"));
    elements.add(new Pair("", "", 0, "section"));
    JsonArray samples = analysis.get("associatedBioreplicates").getAsJsonArray();
    JsonObject sample;
    for (JsonElement _step : samples) {
        sample = _step.getAsJsonObject();
        elements.add(new Pair("Sample", "", 1, "title"));
        elements.add(new Pair("", "", 1, "section"));
        fields = processTemplateFile(templatesDir + File.separator + "bioreplicate-form.json");
        for (Pair field : fields) {
            elements.add(
                    new Pair(field.value, this.getJsonElementAsString(sample.get(field.label)), 2, "field"));
        }

        elements.add(new Pair("Aliquouts", "", 2, "title"));
        elements.add(new Pair("", "", 2, "section"));
        JsonArray aliquots = sample.get("associatedAnalyticalReplicates").getAsJsonArray();
        for (JsonElement aliquot : aliquots) {
            sample = aliquot.getAsJsonObject();
            fields = processTemplateFile(templatesDir + File.separator + "analytical_replicate-form.json");
            for (Pair field : fields) {
                elements.add(new Pair(field.value, this.getJsonElementAsString(sample.get(field.label)), 3,
                        "field"));
            }
        }
    }

    return elements;
}

From source file:client.utils.CommandsSettings.java

License:Apache License

private void parseJson() throws IOException {
    JsonParser parser = new JsonParser();
    if (!this.fo.exists() || !this.fo.exists() || !(this.fi.length() > 0)) {
        this.writeDefault();
    }//  w  w w. j  a  va2 s .c o  m
    JsonElement obj = parser.parse(new FileReader("settings/commands.json"));
    this.commandsObj = obj.getAsJsonObject();
    if (this.commandsObj.toString().contains("null")) {
        System.out.println("Please set up your command settings first");
        System.exit(0);
    }
}

From source file:client.utils.Settings.java

License:Apache License

private void getSettingsFromJson() throws IOException {
    JsonParser parser = new JsonParser();
    if (!this.fo.exists() || !this.fo.exists() || !(this.fi.length() > 0)) {
        this.writeDefault();
    }/*  w  w w.jav  a 2 s. c  o  m*/
    JsonElement obj = parser.parse(new FileReader("settings/config.json"));
    this.settings = obj.getAsJsonObject();
    if (this.settings.toString().contains("null")) {
        System.out.println("Please set up your settings first");
        System.exit(0);
    } else {
        this.user = this.settings.get("username").getAsString();
        this.token = this.settings.get("token").getAsString();
        this.clientid = this.settings.get("clientid").getAsString();
        this.oauth = this.settings.get("oauth").getAsString();
        this.pointsToAdd = this.settings.get("point_increment").getAsInt();
        this.interval = this.settings.get("point_interval").getAsInt();
        JsonArray arr = this.settings.get("channels").getAsJsonArray();
        for (JsonElement chan : arr) {
            channels.add(chan.getAsString());
        }
    }
}

From source file:clientcommunicator.operations.LoginCredentials.java

@Override
public void deserialize(String JSON) throws JSONException {
    JsonElement obj = new JsonParser().parse(JSON);
    this.username = obj.getAsJsonObject().get("username").getAsString();
    this.password = obj.getAsJsonObject().get("password").getAsString();
}

From source file:clientcommunicator.Server.Cookie.java

private JsonObject getUserJsonObject(JsonElement element, boolean setNew) throws MalformedCookieException {
    JsonObject jobject = element.getAsJsonObject();
    if (!jobject.has("playerID")) {
        throw new MalformedCookieException();
    }/* w w w.  j ava  2s. co m*/
    JsonObject resultingCookie = new JsonObject();
    resultingCookie.add("name", jobject.get("name"));
    resultingCookie.add("password", jobject.get("password"));
    resultingCookie.add("playerID", jobject.get("playerID"));
    if (setNew) {
        try {
            String realCookie = resultingCookie.toString();
            realCookie = java.net.URLEncoder.encode(realCookie, "UTF-8");
            this.userInformationString = realCookie;
        } catch (UnsupportedEncodingException ex) {
            Logger.getLogger(Cookie.class.getName()).log(Level.SEVERE, null, ex);
        }
    }
    return jobject;
}

From source file:clocker.mesos.entity.framework.marathon.MarathonFrameworkImpl.java

License:Apache License

@Override
public String startApplication(String id, Map<String, Object> flags) {
    Map<String, Object> substitutions = MutableMap.copyOf(flags);
    substitutions.put("id", id);

    Optional<String> result = MesosUtils.httpPost(this, "v2/apps",
            "classpath:///clocker/mesos/entity/framework/marathon/create-app.json", substitutions);
    if (!result.isPresent()) {
        JsonElement json = JsonFunctions.asJson().apply(result.get());
        String message = json.getAsJsonObject().get("message").getAsString();
        LOG.warn("Failed to start task {}: {}", id, message);
        throw new IllegalStateException("Failed to start Marathon task: " + message);
    } else {//from w  w  w  . ja  va  2s. c om
        LOG.debug("Success creating Marathon task");
        JsonElement json = JsonFunctions.asJson().apply(result.get());
        String version = json.getAsJsonObject().get("version").getAsString();
        return version;
    }
}

From source file:cloud.google.datastore.entity.commit.Commit.java

License:Apache License

private String getTransaction() {
    String result = ConnectionService
            .connect(GCDStatic.getDatastoreApiUrl() + config.getProjectName() + "/beginTransaction").body("")
            .accessToken(AuthenticationFactory.getInstance(config).getAccessToken()).post();
    JsonElement jelement = new JsonParser().parse(result);
    JsonObject jobject = jelement.getAsJsonObject();
    jelement = jobject.get("transaction");
    return jelement != null ? jelement.getAsString() : "";
}