Package com.infoclinika.mssharing.search

Source Code of com.infoclinika.mssharing.search.SpringConfig

/*
* C O P Y R I G H T   N O T I C E
* -----------------------------------------------------------------------
* Copyright (c) 2011-2012 InfoClinika, Inc. 5901 152nd Ave SE, Bellevue, WA 98006,
* United States of America.  (425) 442-8058.  http://www.infoclinika.com.
* All Rights Reserved.  Reproduction, adaptation, or translation without prior written permission of InfoClinika, Inc. is prohibited.
* Unpublished--rights reserved under the copyright laws of the United States.  RESTRICTED RIGHTS LEGEND Use, duplication or disclosure by the
*/
package com.infoclinika.mssharing.search;

import com.infoclinika.msdata.image.SpectrumType;
import com.infoclinika.mssharing.fileserver.StorageService;
import com.infoclinika.mssharing.fileserver.impl.InMemoryStorageService;
import com.infoclinika.mssharing.model.Notifier;
import com.infoclinika.mssharing.model.Searcher;
import com.infoclinika.mssharing.model.internal.CriteriaRules;
import com.infoclinika.mssharing.model.internal.read.Transformers;
import com.infoclinika.mssharing.model.internal.repository.UserRepository;
import com.infoclinika.web.Service;
import com.infoclinika.web.dto.PreCachingResult;
import com.infoclinika.web.dto.TranslationRequest;
import com.infoclinika.web.dto.TranslationResult;
import org.mockito.Matchers;
import org.mockito.invocation.InvocationOnMock;
import org.mockito.stubbing.Answer;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.ImportResource;
import org.springframework.security.crypto.password.PasswordEncoder;
import org.springframework.security.crypto.password.StandardPasswordEncoder;

import javax.persistence.EntityManagerFactory;
import java.util.ArrayList;
import java.util.Collections;

import static org.mockito.Matchers.*;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;

/**
* @author Stanislav Kurilin
*/
@Configuration
@ImportResource({"persistence.cfg.xml", "h2.cfg.xml"})
@ComponentScan(basePackages = {"com.infoclinika.mssharing.model", "com.infoclinika.mssharing.search"})
class SpringConfig {

    @Bean
    public StorageService inMemoryStorage() {
        return new InMemoryStorageService();
    }

    @Bean
    public Notifier notificator() {
        return mock(Notifier.class);
    }

    @Bean
    public Searcher searcher(EntityManagerFactory entityManagerFactory, Transformers transformers, UserRepository userRepository, CriteriaRules criteriaRules) {
        final SearcherImpl searcher = new SearcherImpl(transformers, userRepository, criteriaRules);
        searcher.setEntityManager(entityManagerFactory.createEntityManager());
        searcher.initSearcher();
        return searcher;
    }

    @Bean
    public PasswordEncoder encoder() {
        return new StandardPasswordEncoder();
    }

    @Bean(name = "translationService")
    public Service translationService() {
        Service translationService = mock(Service.class);
        when(translationService.translateFiles(Matchers.<TranslationRequest>anyObject())).thenAnswer(new Answer<TranslationResult>() {
            @Override
            public TranslationResult answer(InvocationOnMock invocation) throws Throwable {
                final TranslationResult result = new TranslationResult();
                result.setTranslatedIds(new ArrayList<Long>(Collections.nCopies(7, 0L)));
                return result;
            }
        });

        when(translationService.preCacheChart(any(Long[].class), anyInt(), anyInt(), any(SpectrumType[].class), anyFloat(),
                anyFloat(), anyDouble(), anyDouble())).thenAnswer(new Answer<PreCachingResult>() {
            @Override
            public PreCachingResult answer(InvocationOnMock invocation) throws Throwable {
                return new PreCachingResult();
            }
        });
        return translationService;
    }

    /*@Bean(name = "sequestSearchService")
    public Service sequestSearchService() {
        Service sequestSearchService = mock(Service.class);
//        final SequestSearchPerFileWrapper sequestSearchPerFileWrapper = new SequestSearchPerFileWrapper(1L, getParams(), "");
//        when(sequestSearchService.sequestSearchPerTranslatedFile(sequestSearchPerFileWrapper)).thenAnswer(new Answer<SequestSearchPerFileResultResponse>() {
//            @Override
//            public SequestSearchPerFileResultResponse answer(InvocationOnMock invocation) throws Throwable {
//                return new SequestSearchPerFileResultResponse(
//                        sequestSearchPerFileWrapper,
//                        new S3ObjectReference("testBucket", "testSqtKey"),
//                        new S3ObjectReference("testBucket", "testSqtDecoyKey"),
//                        new S3ObjectReference("testBucket", "testResultsKey")
//                );
//            }
//        });
        return sequestSearchService;
    }*/

    /*protected static SearchParams getParams() {
        final SearchParams searchParams = new SearchParams();
        final SearchParams.ChangeableCometParams cometParams = new SearchParams.ChangeableCometParams();

        final SearchParams.ChangeableCometParams.CometDatabaseParam db = new SearchParams.ChangeableCometParams.CometDatabaseParam();
        db.setName("Escherichia Coli");
        db.setBucketReference("chorus-development");
        db.setKeyReference("fasta-dbs/EscherichiaColi.fasta");
        cometParams.setDatabase(db);
        cometParams.setPeptideMassTolerance(3.0);
        cometParams.setMaxPrecursorCharge(6);
        cometParams.setPeptideMassUnits(0);
        cometParams.setMassTypeParent(1);
        cometParams.setMassTypeFragment(1);
        cometParams.setPrecursorToleranceType(0);
        cometParams.setSearchEnzymeNumber(0);
        cometParams.setNumEnzymeTermini(1);
        cometParams.setSearchEnzymeNumber(0);
        searchParams.setCometParams(cometParams);

        final SearchParams.Ms2ProcessorParams ms2ProcessorParams = new SearchParams.Ms2ProcessorParams();
        ms2ProcessorParams.setIsolationWidth(200000);
        ms2ProcessorParams.setMaxCharge(7);

        searchParams.setMs2ProcessorParams(ms2ProcessorParams);
        final SearchParams.PercolatorParams percolatorParams = new SearchParams.PercolatorParams();
        percolatorParams.setPercolatorParam(3);
        searchParams.setPercolatorParams(percolatorParams);
        return searchParams;
    }*/

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