JobMongoDBAdaptorTest.java

/*
 * Copyright 2015-2016 OpenCB
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *     http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */

package org.opencb.opencga.catalog.db.mongodb;

import org.junit.Test;
import org.opencb.commons.datastore.core.Query;
import org.opencb.commons.datastore.core.QueryOptions;
import org.opencb.commons.datastore.core.QueryResult;
import org.opencb.opencga.catalog.db.api.JobDBAdaptor;
import org.opencb.opencga.catalog.exceptions.CatalogDBException;
import org.opencb.opencga.catalog.exceptions.CatalogException;
import org.opencb.opencga.catalog.models.Job;
import org.opencb.opencga.core.common.TimeUtils;

import java.util.*;

import static org.junit.Assert.*;

/**
 * Created by pfurio on 3/2/16.
 */
public class JobMongoDBAdaptorTest extends MongoDBAdaptorTest {

    @Test
    public void createJobTest() throws CatalogDBException {
        Job job = new Job();
        job.setVisits(0);

        long studyId = user3.getProjects().get(0).getStudies().get(0).getId();
        job.setName("jobName1");
        System.out.println(catalogJobDBAdaptor.insert(job, studyId, null));
//        long analysisId = catalogDBAdaptor.getAnalysisId(studyId, "analysis1Alias");

        job.setName("jobName2");
        System.out.println(catalogJobDBAdaptor.insert(job, studyId, null));
        try {
            catalogJobDBAdaptor.insert(job, -1, null);
            fail("error: expected exception");
        } catch (CatalogDBException e) {
            System.out.println("correct exception: " + e);
        }
    }

    @Test
    public void deleteJobTest() throws CatalogException {
        long studyId = user3.getProjects().get(0).getStudies().get(0).getId();

        Job job = catalogJobDBAdaptor.insert(new Job("name", user3.getId(), "", "", "", 4, Collections.<Long>emptyList
                ()), studyId, null).first();
        long jobId = job.getId();
        assertEquals(Job.JobStatus.PREPARED, job.getStatus().getName());
        catalogJobDBAdaptor.delete(jobId);

        thrown.expect(CatalogDBException.class);
        thrown.expectMessage("not exist");
        catalogJobDBAdaptor.get(jobId, QueryOptions.empty());
    }

    @Test
    public void getAllJobTest() throws CatalogDBException {
        long studyId = user3.getProjects().get(0).getStudies().get(0).getId();
        QueryResult<Job> allJobs = catalogJobDBAdaptor.getAllInStudy(studyId, null);
        System.out.println(allJobs);
    }


    @Test
    public void getJobTest() throws CatalogException {
        long studyId = user3.getProjects().get(0).getStudies().get(0).getId();

        Job job = catalogJobDBAdaptor.insert(new Job("name", user3.getId(), "", "", "", 4, Collections.<Long>emptyList
                ()), studyId, null).first();
        long jobId = job.getId();

        job = catalogJobDBAdaptor.get(jobId, null).first();
        System.out.println(job);

        try {
            catalogJobDBAdaptor.get(-1, null);
            fail("error: expected exception");
        } catch (CatalogDBException e) {
            System.out.println("correct exception: " + e);
        }

    }

    @Test
    public void incJobVisits() throws CatalogException {
        long studyId = user3.getProjects().get(0).getStudies().get(0).getId();
        Job jobBefore = catalogJobDBAdaptor.insert(new Job("name", user3.getId(), "", "", "", 4, Collections
                .<Long>emptyList()), studyId, null).first();
        long jobId = jobBefore.getId();

        Long visits = (Long) catalogJobDBAdaptor.incJobVisits(jobBefore.getId()).first().get("visits");

        Job jobAfter = catalogJobDBAdaptor.get(jobId, null).first();
        assertTrue(jobBefore.getVisits() == jobAfter.getVisits() - 1);
        assertTrue(visits == jobAfter.getVisits());
    }

    @Test
    public void getJobsOrderedByDate() throws CatalogDBException {
        long studyId = user3.getProjects().get(0).getStudies().get(0).getId();

        // Job with current date
        Job job1 = new Job();
        job1.setName("job1");
        job1.setCreationDate(TimeUtils.getTime());

        // Job with current date one hour before
        Calendar cal = Calendar.getInstance();
        cal.setTime(new Date());
        cal.add(Calendar.HOUR, -1);
        Date oneHourBack = cal.getTime();

        Job job2 = new Job();
        job2.setName("job2");
        job2.setCreationDate(TimeUtils.getTime(oneHourBack));

        // We create the jobs
        catalogJobDBAdaptor.insert(job1, studyId, new QueryOptions());
        catalogJobDBAdaptor.insert(job2, studyId, new QueryOptions());

        // Obtain the jobs in descending order
        QueryOptions queryOptions = new QueryOptions()
                .append(QueryOptions.SORT, JobDBAdaptor.QueryParams.CREATION_DATE.key())
                .append(QueryOptions.ORDER, QueryOptions.DESCENDING);


        QueryResult<Job> jobQueryResult1 = catalogJobDBAdaptor.get(new Query(), queryOptions);

        assertTrue("job1".equals(jobQueryResult1.getResult().get(0).getName()));
        assertTrue("job2".equals(jobQueryResult1.getResult().get(1).getName()));

        // Obtain the jobs in ascending order
        queryOptions = new QueryOptions()
                .append(QueryOptions.SORT, JobDBAdaptor.QueryParams.CREATION_DATE.key())
                .append(QueryOptions.ORDER, QueryOptions.ASCENDING);

        QueryResult<Job> jobQueryResult2 = catalogJobDBAdaptor.get(new Query(), queryOptions);

        assertTrue("job2".equals(jobQueryResult2.getResult().get(0).getName()));
        assertTrue("job1".equals(jobQueryResult2.getResult().get(1).getName()));
    }

    @Test
    public void extractFilesFromJobs() throws Exception {
        Job job = new Job();
        job.setOutDirId(5);
        job.setInput(Arrays.asList(1L, 2L, 3L, 4L));
        job.setOutput(Arrays.asList(6L, 7L, 8L, 9L));
        long studyId = user3.getProjects().get(0).getStudies().get(0).getId();
        job.setName("jobName1");
        QueryResult<Job> insert = catalogJobDBAdaptor.insert(job, studyId, null);

        List<Long> longList = Arrays.asList(1L, 3L, 5L, 6L, 8L);
        catalogJobDBAdaptor.extractFilesFromJobs(new Query(JobDBAdaptor.QueryParams.STUDY_ID.key(), studyId), longList);

        QueryResult<Job> jobQueryResult = catalogJobDBAdaptor.get(insert.first().getId(), QueryOptions.empty());
        assertEquals(-1L, jobQueryResult.first().getOutDirId());

        assertTrue(jobQueryResult.first().getInput().containsAll(Arrays.asList(2L, 4L)));
        assertEquals(2, jobQueryResult.first().getInput().size());

        assertTrue(jobQueryResult.first().getOutput().containsAll(Arrays.asList(7L, 9L)));
        assertEquals(2, jobQueryResult.first().getOutput().size());
    }

}