com.epam.ngb.cli.manager.command.handler.http.AbstractAnnotationReferenceHandler.java Source code

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Here is the source code for com.epam.ngb.cli.manager.command.handler.http.AbstractAnnotationReferenceHandler.java

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/*
 * MIT License
 *
 * Copyright (c) 2017 EPAM Systems
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in all
 * copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 * SOFTWARE.
 */

package com.epam.ngb.cli.manager.command.handler.http;

import com.epam.ngb.cli.app.ApplicationOptions;
import com.epam.ngb.cli.constants.MessageConstants;
import com.epam.ngb.cli.entity.BiologicalDataItem;
import com.epam.ngb.cli.exception.ApplicationException;
import com.epam.ngb.cli.manager.request.RequestManager;
import org.apache.http.client.methods.HttpPut;
import org.apache.http.client.utils.URIBuilder;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.net.URISyntaxException;
import java.util.ArrayList;
import java.util.List;

import static com.epam.ngb.cli.constants.MessageConstants.ILLEGAL_COMMAND_ARGUMENTS;

/**
 * {@code {@link AbstractAnnotationReferenceHandler }} represents a parent for two tools
 * {@see AnnotationReferenceAddingHandler, AnnotationReferenceRemovingHandler }
 * - reference ID or name
 * - annotation file IDs, names or paths to files (only for registration as a new file)
 */
public abstract class AbstractAnnotationReferenceHandler extends AbstractHTTPCommandHandler {

    private static final Logger LOGGER = LoggerFactory.getLogger(AbstractAnnotationReferenceHandler.class);

    private Long referenceId;
    private List<Long> annotationFileIds;

    /**
     * If true command will output result of reference registration in a json format
     */
    private boolean printJson;
    /**
     * If true command will output result of reference registration in a table format
     */
    private boolean printTable;

    @Override
    public void parseAndVerifyArguments(List<String> arguments, ApplicationOptions options) {
        annotationFileIds = new ArrayList<>(arguments.size() - 1);
        if (arguments.size() < 2) {
            throw new IllegalArgumentException(
                    MessageConstants.getMessage(ILLEGAL_COMMAND_ARGUMENTS, getCommand(), 2, arguments.size()));
        }
        referenceId = loadReferenceId(arguments.get(0));
        for (int i = 1; i < arguments.size(); i++) {
            try {
                annotationFileIds.add(loadFileByNameOrBioID(arguments.get(i)).getBioDataItemId());
            } catch (ApplicationException e) {
                LOGGER.debug(e.getMessage(), e);

                ApplicationOptions registerOptions = new ApplicationOptions();
                registerOptions.setDoIndex(options.isDoIndex());

                FileRegistrationHandler handler = new FileRegistrationHandler(arguments.get(i), referenceId, this,
                        registerOptions);
                handler.setRequestUrl(handler.getServerParameters().getRegistrationUrl());
                handler.setRequestType("POST");

                BiologicalDataItem registeredFile = handler.registerItems().get(0);
                annotationFileIds.add(registeredFile.getBioDataItemId());
            }
        }
        printJson = options.isPrintJson();
        printTable = options.isPrintTable();
    }

    @Override
    public int runCommand() {
        String url = serverParameters.getServerUrl() + getRequestUrl();
        for (Long annotationFileId : annotationFileIds) {
            try {
                URIBuilder builder = new URIBuilder(String.format(url, referenceId));
                builder.addParameter("annotationFileId", String.valueOf(annotationFileId));
                builder.addParameter("remove", String.valueOf(isRemoving()));
                HttpPut put = new HttpPut(builder.build());
                setDefaultHeader(put);
                if (isSecure()) {
                    addAuthorizationToRequest(put);
                }
                String result = RequestManager.executeRequest(put);
                checkAndPrintRegistrationResult(result, printJson, printTable);
            } catch (URISyntaxException e) {
                throw new ApplicationException(e.getMessage(), e);
            }
        }
        return 0;
    }

    protected abstract boolean isRemoving();
}